RetrogeneDB ID: retro_ecab_250

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:4452120..4452507(+)
• Located in intron of: ENSECAG00000012486

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V1
• Ensembl ID: ENSECAG00000011858
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 1 [Source:HGNC Symbol;Acc:12494]

Sequence

>retro_ecab_250
GTAAAATTTACCCCAAATTTTCACTCCCTGGGAGAACTTGAAGAAGGCCAAAGATTAGGTGATAGTACAGTTAGCTGGAG
TCTCTAAGACGATGAAGATATGTTGCTTACAAGGTGGACAGCCATATAATTGGGCCTCCAAGGACAAATTACAAAAACAA
ATATATCGCCTCAAAATGGCAAGTGAATCTAAATACCCAGAAGCTCCCTTATCCTTTAGATTTGTAACAAAAAGTAGTAT
GAATGGAATAAGTAATCCAGTAGAATGGTGGATATACAGAGCATACCATCCAGTGTTAGCAAAGTAACAAAATACAAAAC
CAATAAAGTTGCATTTTCAGATCTAAGACATTTAATGATGTCCAAAGAATATACGAAACTTCTGCAG

Alignment

ORF - retro_ecab_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.22 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGM-IIGPPRTIYENR-IYSLKIECGPKYP
          VK...NF..L.ELEEGQ...GD.TVSW.L.DDEDM.LTRWT...IIGPPRT.Y.N..IY.LK.....KYP
Retrocopy VKFTPNFHSLGELEEGQR-LGDSTVSWSL*DDEDMLLTRWTAI<IIGPPRTNYKNK<IYRLKMASESKYP

Parental  EAPPFVRFVTKINMNGVNS-SNGVVDPRAI-SVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQ
          EAP...RFVTK..MNG....S...VD...I.S...K.......KV....LR.LMMSKE..KL.Q
Retrocopy EAPLSFRFVTKSSMNGISN<SSRMVDIQSIPSSVSKVTKYKTNKVAFSDLRHLMMSKEYTKLLQ

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	10.21 RPM
SRP021940_cerebellum	0.00 RPM	35.26 RPM
SRP021940_embryo	0.03 RPM	37.75 RPM
SRP021940_placental_villous	0.00 RPM	35.17 RPM
SRP021940_synovial_membrane	0.00 RPM	19.99 RPM
SRP021940_testis	0.00 RPM	56.46 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_250 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_250 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011858	3 retrocopies	retro_ecab_1112, retro_ecab_250 , retro_ecab_900,
Homo sapiens	ENSG00000244687	4 retrocopies	retro_hsap_2175, retro_hsap_2440, retro_hsap_2884, retro_hsap_4192,
Macaca mulatta	ENSMMUG00000012228	6 retrocopies	retro_mmul_1722, retro_mmul_2382, retro_mmul_351, retro_mmul_436, retro_mmul_629, retro_mmul_907,
Otolemur garnettii	ENSOGAG00000025894	12 retrocopies	retro_ogar_1381, retro_ogar_1391, retro_ogar_153, retro_ogar_1637, retro_ogar_1929, retro_ogar_2027, retro_ogar_2478, retro_ogar_2984, retro_ogar_3172, retro_ogar_3338, retro_ogar_620, retro_ogar_80,
Pan troglodytes	ENSPTRG00000013615	1 retrocopy	retro_ptro_64,
Rattus norvegicus	ENSRNOG00000025580	21 retrocopies	retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,
Ictidomys tridecemlineatus	ENSSTOG00000014322	6 retrocopies	retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452, retro_itri_1600, retro_itri_992,