RetrogeneDB ID: retro_ecab_675

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:24073932..24074605(+)
• Located in intron of: ENSECAG00000016889

Retrocopy information

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

Parental gene information

• Parental gene symbol: SET
• Ensembl ID: ENSECAG00000009117
• Aliases: None
• Description: SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]

Sequence

>retro_ecab_675
GAAAAAGAACGGCAAGAAGTAGCAGGAAACAATGATGAAATACAAAATGAAACAGACAGACTTACTGAACAGGCCAGTGA
GGAGATTTTGAAAGTAGAACAGAAATATAACAAACTCCATCAACCATTTTTTCACAAGAGGTCAGAATTAATTGCCAAAA
TCCCATATTATGGCGTAACAACCTTTGTCAGCCACCCGCAAGTCTGCACTGCTTGGGGAGGAGGATGAAGAGGTGGTGCA
TTATTCGACCACAGTTGAAGCGACAGAATTTGAAGGTGTAAAATCGGGTTACAGAATAGATTTTCATCTTGATGAAAATG
TTCACTTCAAAAAATAAAGTTCTCTCCCAAGAATTTTATCTGAATGAGAGTGACGGTCCATCTTCAAAGCCCACTGAAAT
CAAAAGGAAATCTGAAAAGGATCTGATGGAATATTCAAGTCAAATGCAGAAGAAAGCCAACAGGAAGTAGCAGCAGGGGG
CACCAGAGAGCTTCTCTCCCCGGTTTACTGACCCTTCTGATGTAGGTGCAGATGCTTTAGGAGAGGTCATCAAAGATGGT
ATTTGGCCAAATTCACTACGGTACTACTTGGTTCCTGACATGTAGAGAAGGAATAAAGGCAAGGCGAAGATAATGGTGCT
GAGGCTGAAGAAGAAAAATTGGAAGATGTTGAT

Alignment

ORF - retro_ecab_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.5 %
• Parental protein coverage: 88.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNF-WVTTFVNHP-QV
          EKE.QE.....DE.QNE.DRL.EQASEEILKVEQKYNKL.QPFF.KRSELIAKIP...W.......P...
Retrocopy EKERQEVAGNNDEIQNETDRLTEQASEEILKVEQKYNKLHQPFFHKRSELIAKIPYY<WRNNLCQPP<RK

Parental  SALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFE-NKILSKEFHLNESGDPSSKSTEIKWK
          SALLGEEDEE..HY.T.VE.TEFE..KSGYRIDF..DEN..F..NK.LS.EF.LNES..PSSK.TEIK.K
Retrocopy SALLGEEDEEVVHYSTTVEATEFEGVKSGYRIDFHLDENVHFK>NKVLSQEFYLNESDGPSSKPTEIKRK

Parental  SGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVPDM-DDEEG
          S.KDL...SSQ.Q.KA.RK.Q...PESF...FTD.SD.GAD.LGEVIKD.IWPN.L.YYLVPDM....E.
Retrocopy SEKDLMEYSSQMQKKANRK*QQGAPESFSPRFTDPSDVGADALGEVIKDGIWPNSLRYYLVPDM<VEKE*

Parental  EGEEDDDDDEEEEGLEDID
          ...ED.....EEE.LED.D
Retrocopy RQGEDNGAEAEEEKLEDVD

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	0.12 RPM	51.24 RPM
SRP021940_cerebellum	0.42 RPM	73.48 RPM
SRP021940_embryo	0.38 RPM	174.00 RPM
SRP021940_placental_villous	0.10 RPM	70.39 RPM
SRP021940_synovial_membrane	0.25 RPM	54.90 RPM
SRP021940_testis	0.00 RPM	43.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_675 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 113 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Equus caballus	ENSECAG00000009117	4 retrocopies	retro_ecab_358, retro_ecab_417, retro_ecab_505, retro_ecab_675 ,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,