SHIELD | Shared Harvard Inner-Ear Laboratory Database

MOUSE GENE INFORMATION [PubMed]

Description

collagen, type IX, alpha 1

Synonyms

Col9a-1

Chromosome

Genetic Map Distance

9.95 cM

RefSeq Accessions

NM_007740; NP_031766

NCBI Entrez Gene

12839 at chr1:24184449-24259577 (mm9) / chr1:24177588-24252738 (mm10)

Ensembl Gene

ENSMUSG00000026147

VEGA Gene

OTTMUSG00000022796

MGI Gene

MGI:88465

Mouse Protein (8)

UniProt ID	Description	Length (AA)	Predicted # TMs
Q05722	Collagen alpha-1(IX) chain	921	1
Q80VN9	Col9a1 protein	629	1
Q8BSQ4	Putative uncharacterized protein	921	1
Q8BT32	Putative uncharacterized protein (Fragment)	167	0
Q8CEP0	Putative uncharacterized protein (Fragment)	45	0
Q9CT83	Putative uncharacterized protein	155	0
Q9D0D2	Col9a1 protein	680	0
Q9WUX8	Alpha 1 type IX collagen short form (Fragment)	26	0

Pfam Domains

Laminin_G_2; Pfam-B_544; Collagen; Collagen; Collagen; Collagen; Pfam-B_544; Collagen; Pfam-B_544; Collagen; Pfam-B_544; Collagen; Collagen; Pfam-B_5239; Collagen; Pfam-B_544; Collagen; Collagen; Collagen

Mouse alleles (1)

Allele Name	Allele Type
Col9a1^tm1Jae	Targeted (knock-out)

Human Homolog

COL9A1 (collagen, type IX, alpha 1)

Human synonyms

DJ149L1.1.2; EDM6; MED; STL4

Human cytoband

6q12-q14

Known deafness gene

STL

Within mapped deafness loci

Associated Human Disease in OMIM

Osteoarthritis Susceptibility 1; OS1 [OA|Osteoarthritis of Hip, Female-Specific, Susceptibility to|Osteoarthrosis]

Chicken homolog (6)

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000025686

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000036261

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000036262

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000036263

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000036264

ENSGALG00000015970 (CO9A1_CHICK) encoding ENSGALP00000036267

Gene Ontology

Biological Process (4)	cartilage development; growth plate cartilage development; growth plate cartilage development; tissue homeostasis
Cellular Component (4)	extracellular region; collagen; proteinaceous extracellular matrix; collagen type IX
Molecular Function (1)	metal ion binding

FACS-Sorted Hair Cells

Data | Chart

	E16a	E16b	P0	P4	P7	P16
Utricle GFP+ cells	1787	4196	1256	691	1241	124
Cochlea GFP+ cells	640	3616	620	1599	933	NA
Utricle GFP- cells	3118	13565	18787	12154	28322	5459
Cochlea GFP- cells	2334	5276	17762	15501	28713	NA

Analysis

Condition A	Mean A	Condition B	Mean B	Fold Change (B/A)	False Discovery Rate (FDR)
GFP-	13727	GFP+	1518	0.11	0.000931
Utricle	7558	Cochlea	7699	1.02	1
Embryonic	4316	Postnatal	9512	2.20	0.296

Adult Cochlear Inner and Outer Hair Cells

Probeset ID	IHC (mean ± sd)	OHC (mean ± sd) [OHC replicate]	Fold Change (OHC/IHC)	False Discovery Rate (FDR)
17211458	7.46 ± 1.36	8.96 ± 0.47 [9.99]	1.20	0.552

Otic Progenitor Cells

Data

Growth Factor	Replicate 1	Replicate 2	Replicate 3	Mean
bFGF	8	3	0	2
No bFGF	6	11	3	5
EGF	10	11	9	10

Analysis

Condition A	Mean A	Condition B	Mean B	Fold Change (B/A)	False Discovery Rate (FDR)
bFGF	2	No bFGF	5	1.80	1
bFGF	2	EGF	10	3.57	0.0147
No bFGF	5	EGF	10	1.99	0.106

Chicken Stereocilium Proteomics

Protein ID	ENSGALP00000025686
Symbol	COL9A1
Description	Collagen, type IX, alpha 1
log10 riBAQ in stereocilia (mean ± sd)	ND
log10 riBAQ in utricle (mean ± sd)	-4.98 ± 0.14
Molecules per stereocilium (mean ± error with slope error)	ND
Corrected Molecules per stereocilium (mean ± sd)	ND
Stereocilium / Utricle ratio (mean ± sd)	UTR only
Enriched in the stereocilia (FDR < 0.05)	NA

Auditory and Vestibular Ganglion Neurons

Probe set ID: 1421381_a_at

Age	E12	E13	E16	P0	P6	P15
Spiral ganglion
Replicate 1	1025.21	790.33	812.36	987.4	653.54	861.28
Replicate 1 Call	A	A	A	M	P	A
Replicate 2	938.02	949.72	882.86	1184.7	967.77	712.45
Replicate 2 Call	A	A	A	P	P	A
Replicate 3	1101.84	857.06	866.57	1116.68	920.63	800.09
Replicate 3 Call	A	A	A	A	P	A
Replicate 4			852.62	1088.25	1114.75	1085.48
Replicate 4 Call			A	A	P	A
Mean	1021.69	865.7	853.6	1094.26	914.17	864.83
Standard Deviation	81.97	80.05	30.14	81.93	192.42	159.28
Log2 Mean	9.99	9.75	9.74	10.09	9.81	9.74
Log2 Standard Deviation	0.12	0.13	0.05	0.11	0.33	0.26

Vestibular ganglion
Replicate 1	1117	1043.02	1724.45	1387.62	1307.79	724.42
Replicate 1 Call	A	A	A	A	M	P
Replicate 2	1034.57	1033.82	1101.19	1392.1	1221.28	880.97
Replicate 2 Call	A	A	M	A	P	A
Replicate 3	1179.45	1176.9	1249.84	1353.27	1189.6	842.96
Replicate 3 Call	A	A	A	A	P	A
Mean	1110.34	1084.58	1358.49	1377.66	1239.56	816.12
Standard Deviation	72.67	80.08	325.53	21.24	61.18	81.65
Log2 Mean	10.11	10.08	10.38	10.43	10.27	9.67
Log2 Standard Deviation	0.09	0.1	0.33	0.02	0.07	0.15

Probe set ID: 1428571_at

Age	E12	E13	E16	P0	P6	P15
Spiral ganglion
Replicate 1	1342.95	1936.91	666.94	5143.03	9611.64	4337.64
Replicate 1 Call	P	P	P	P	P	P
Replicate 2	1354.5	1837.83	1578.19	8157.39	7066.61	4507.04
Replicate 2 Call	P	P	P	P	P	P
Replicate 3	1387.58	2040.9	732.08	1886.89	9435.47	4448.89
Replicate 3 Call	P	P	P	P	P	P
Replicate 4			2361.59	1204.04	9177.91	3970.28
Replicate 4 Call			P	P	P	P
Mean	1361.68	1938.55	1334.7	4097.84	8822.91	4315.96
Standard Deviation	23.16	101.54	800.59	3205.97	1184.33	240.93
Log2 Mean	10.41	10.92	10.18	11.61	13.1	12.07
Log2 Standard Deviation	0.02	0.08	0.88	1.27	0.21	0.08

Vestibular ganglion
Replicate 1	1715.23	1792.6	4281.61	4727.07	4251.03	3832.95
Replicate 1 Call	P	P	P	P	P	P
Replicate 2	1754.81	1853.75	4463.68	4476.49	7279.82	2244.67
Replicate 2 Call	P	P	P	P	P	P
Replicate 3	1639.45	1911.52	3406.6	2952.25	5974.79	2837.99
Replicate 3 Call	P	P	P	P	P	P
Mean	1703.16	1852.62	4050.63	4051.94	5835.21	2971.87
Standard Deviation	58.62	59.47	565.13	960.56	1519.21	802.56
Log2 Mean	10.73	10.85	11.97	11.95	12.48	11.5
Log2 Standard Deviation	0.05	0.05	0.21	0.37	0.39	0.39

GENE VIEW

Col9a1