RetrogeneDB ID: retro_ecab_419

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:40513731..40514898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSECAG00000014334
• Aliases: None
• Description: Elongation factor 1-gamma [Source:UniProtKB/Swiss-Prot;Acc:A2Q127]

Sequence

>retro_ecab_419
ATGACAGCTGGGACCTTGTAGACATATCCTGAAAACTGGAAGGCCTTCCAGGCTCTGACAGCCGCCCAGTACAGTGGAGC
TCAGGTCCGTGTGCTGTCTGCACGATCCACTTCCAGTTCGGCCAAACCAACTGCACCCCTGAATTTCTCCATAAATTTCC
TACTGGCAAGTTTTCAGCATTTGAGGGTGATGACAGATTCTTGTGTTTGAGAGCGATGCCATTGTCTACCATACTAGCAA
TGAGGAGCTGCAGGGAAGTGCTTCAGAGGCAGCAGCCTCTGTGGTGCAGTGGATGAACTTTGCTGATAGTAACATAGTAC
CCCCAGCCAGTACCTGATGGTTCCCCACCTTGAGCATCATGTACCACAATAAGCAGGCCACAGAGAACGCAAAGGAGGAG
GTGAGGTGAATTCCGAGGTTATTAGATGCTCACTTGAAAATGAGGACTTTTCTGGTGGTGAACTGTGACACTGGCTGACG
TCACAGTTGTCTGCACTCTACTTTGGCTGTATAAACAGGCATTGGTGGCTTCTTTTCGCCAGGCCTTTCCCAATACCAAC
TGCTGCTTCCTCATCTGCACTACCAGTTCCACTTCCGAGTTGTCTTGGGAGAGGTGAAAATCTGTGAGAAGACGTCCCAG
TTTGGTGCTAAAAAGTTTACAGATAGCCAGCTTTAAAAGGACACCCCATGGAAAGAGAAAGGTTCATGTGAGGAAAGCAG
AAGCCCCAGGCTGAGGAGGAAAAGGAGAAAAAGGTGGCTGCCCCTAGTCCCGAGGAGGAGGTGGGTAAACGTGCAGGCTC
TGTTTGCTGAACCAAAGGCCAAAGACCCCTTTGTTCATCTGACCAAGAGTACGTTTGTGTCGGGTAAATTTAAATCAAGT
ACTCCAAAGATGACACAATCTGTGACATTGCTGTATTTTGGGGACCACTTTGATAAGGATGGCTGATCCTTGTGATACTC
GAGGACTGCTTCCCTGAAGAACTCACCCAAACGTTCATGAGTTGCCTCATCATCACTGGAGTGTTCCAGTGACTGGGCAA
GCTGAGGAAGAATGCTTTTGCCAGTGTCACCCTCTTTGGAACCAACAATAGCAGCCCCATTTCAGGAGTTCAGATCTTCT
GAGTCTAGGAGCTTGCCTTTCCTGTGAGTCCAGATTGGCAGGTAGAC

Alignment

ORF - retro_ecab_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 89.93 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPP-HFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFC-
          M.AGTL.TYPENW.AF.AL.AAQYSGAQVRVLSA...HF.FGQTN.TPEFL.KFP.GK..AFEGDD.F..
Retrocopy MTAGTL*TYPENWKAFQALTAAQYSGAQVRVLSARS<HFQFGQTNCTPEFLHKFPTGKFSAFEGDDRFL<

Parental  VFESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRI
          VFES.AI.Y..SNEEL.GS..EAAA.VVQW..FADS.IVPPAST..FPTL.IM.HNKQATENAKEEVR.I
Retrocopy VFESDAIVYHTSNEELQGSASEAAASVVQWMNFADSNIVPPAST*WFPTLSIMYHNKQATENAKEEVR*I

Parental  LGLLDAHLKTRTFLV-GE-RVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCIN-QPQFRAVLG
          ..LLDAHLK.RTFLV.GE..VTLAD.TVVCTLLWLYKQ.L..SFRQAFPNTN..FL.C...Q..FR.VLG
Retrocopy PRLLDAHLKMRTFLV<GE<TVTLADVTVVCTLLWLYKQALVASFRQAFPNTNCCFLICTT<QFHFRVVLG

Parental  EVKLCEKMAQFDAKKFAESQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPK
          EVK.CEK..QF.AKKF..SQ..KDTP.KEKGS.EE...P...RK..K......P........QAL.AEPK
Retrocopy EVKICEKTSQFGAKKFTDSQL*KDTPWKEKGSCEESRSPRLRRKRRKRWLPLVPRRRWVNV-QALFAEPK

Parental  AKDPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYS-EYRFPEELTQTFMSCNLITG
          AKDPF.HL.KSTFV...FK.......T.SV.L.YF..HFDKDG.SL.YS.E..FPEELTQTFMSC..ITG
Retrocopy AKDPFVHLTKSTFVSGKFKSS-TPKMTQSVTLLYFGDHFDKDG*SL*YS<EDCFPEELTQTFMSCLIITG

Parental  MFQRLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVD
          .FQ.L.KLRKNAFASV.LFGTNNSS.ISGV..F...ELAFP.SPDWQVD
Retrocopy VFQ*LGKLRKNAFASVTLFGTNNSSPISGVQIF*V*ELAFPVSPDWQVD

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	0.06 RPM	1823.55 RPM
SRP021940_cerebellum	0.00 RPM	600.03 RPM
SRP021940_embryo	0.97 RPM	1262.04 RPM
SRP021940_placental_villous	0.14 RPM	446.95 RPM
SRP021940_synovial_membrane	0.69 RPM	1023.03 RPM
SRP021940_testis	0.32 RPM	894.44 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_419 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_419 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419 ,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,