RetrogeneDB ID: retro_ecab_294

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:25828493..25828774(+)
• Located in intron of: ENSECAG00000020285

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015464
• Aliases: None
• Description: None

Sequence

>retro_ecab_294
GTGAACTTTCCTAAAACCTGCTTGACTTTCTGAAAGAAGTAGAGAAAACACCAACCTCACAAAATGACACAGTATAAGAG
GGCAAGGACCCTCCATATGCCCAGGGAAAGTGACATGACAGAAAGCAGAGTGGCTATAGGAGGCAGACTAAGCATATTTT
CTCCAAAAAGTCTAAAACCACAAAGATTGTGCTGAGGCTTGAATACATTGAGCCCAACTGCAGATCTAAGAGAATGCTGG
CTGTTAAGAGATGTAAGCATTTTGAGCTGGGAGGAGATAAG

Alignment

ORF - retro_ecab_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.29 %
• Parental protein coverage: 90.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNVPKTRRTFCKKCGKHQPHKVTQYKK-GKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
          VN.PKT..TF.KK..KHQPHK.TQYK..GKD..YAQGK...DRKQSGY..QTK.IF.KK.KTTK.IVLRL
Retrocopy VNFPKTCLTF*KK*RKHQPHKMTQYKR<GKDPPYAQGK*-HDRKQSGYRRQTKHIFSKKSKTTK-IVLRL

Parental  ECVEPNCRSKRMLAIKRCKHFELGGDK
          E..EPNCRSKRMLA.KRCKHFELGGDK
Retrocopy EYIEPNCRSKRMLAVKRCKHFELGGDK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	192.20 RPM
SRP021940_cerebellum	0.00 RPM	63.05 RPM
SRP021940_embryo	0.00 RPM	187.12 RPM
SRP021940_placental_villous	0.00 RPM	121.14 RPM
SRP021940_synovial_membrane	0.00 RPM	138.85 RPM
SRP021940_testis	0.00 RPM	58.12 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_294 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_294 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009384	1 retrocopy	retro_amel_85,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294 , retro_ecab_543, retro_ecab_646,
Felis catus	ENSFCAG00000015397	3 retrocopies	retro_fcat_106, retro_fcat_25, retro_fcat_80,
Homo sapiens	ENSG00000241343	14 retrocopies	retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2, retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Homo sapiens	ENSG00000257529	1 retrocopy	retro_hsap_1353,
Gorilla gorilla	ENSGGOG00000009460	6 retrocopies	retro_ggor_13, retro_ggor_152, retro_ggor_207, retro_ggor_208, retro_ggor_42, retro_ggor_5,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mus musculus	ENSMUSG00000079435	1 retrocopy	retro_mmus_4,
Nomascus leucogenys	ENSNLEG00000007540	27 retrocopies	retro_nleu_1003, retro_nleu_1243, retro_nleu_1291, retro_nleu_153, retro_nleu_157, retro_nleu_1632, retro_nleu_178, retro_nleu_1833, retro_nleu_1903, retro_nleu_1959, retro_nleu_2145, retro_nleu_2345, retro_nleu_2381, retro_nleu_2699, retro_nleu_2965, retro_nleu_2995, retro_nleu_2996, retro_nleu_3027, retro_nleu_3028, retro_nleu_3059, retro_nleu_3111, retro_nleu_385, retro_nleu_453, retro_nleu_644, retro_nleu_805, retro_nleu_842, retro_nleu_991,
Otolemur garnettii	ENSOGAG00000004551	6 retrocopies	retro_ogar_1160, retro_ogar_1681, retro_ogar_2390, retro_ogar_2519, retro_ogar_294, retro_ogar_470,
Pongo abelii	ENSPPYG00000025837	37 retrocopies	retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011, retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Tursiops truncatus	ENSTTRG00000012779	1 retrocopy	retro_ttru_5,