RetrogeneDB ID: retro_ecab_1092

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:116291333..116292647(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000020943
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ELL2
• Ensembl ID: ENSECAG00000022933
• Aliases: None
• Description: elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]

Sequence

>retro_ecab_1092
ATCAAAATCCCCCCAAACAATTCACCAACTGATGTATCCAACTTTAACTTTCAATTGTCAAATGTGAGTAAAGACAACCA
TCAAGACCATACTCAACAAACTGTCTCAGGCTATAGTCCCTCACAGCTCAGTTGGCTGCACTTGAGGCGAGATAAAATGA
CGCAGTGTAGAACAACCAATGCTTCTCAGATAACACCAGTAAGAACCCAGGCAGAAGAGGAATCCTGCAACAAATGGAAA
AAAATTGGAAAGCCATGTGGAAAGAAAAGAATGCCAATTCGGAAAGCACCTCAAGCCATTCCAGATCCAGTGCCTGAGAG
AAAAAGAACAGCGCCCCTTAACCCTGCATACACAATTCGAAAATCACGAGTTCCCAACAGTGTCCGCTTGCGGCCATATA
GGGACAGGGTGATTCACTTACTGGCATTGAAGGACTACAAGAAAACAGAACTGCTTTTTCGACTTCGGAAAGATGGTGTG
GAACAAAATGACGAGAACTCCCTTGAAAATATCCTAAACCAAGTAGCCAATCTGAATACTCAGGATTTTTCATATACCTT
AAAGGATTATGTATTTAAAGAACTCCAAAGAGACTGGCCTGGATACAGTGAACTGGACAAGCAGTCATTGGAGTTGGTGC
TTTCCCAAAGAGTAGATCCATTTCAGAATGCTACTGACATTAATCACTCAGAATCTTCTATAGGTTCTAGTACAAATGAA
ACATCATCTCCTCAGAAATGGCTTTTCAATTCTGCTGTTATTGATCCTTTAAAGAAAAAGAAAGTCAGAATATCTCACCT
GACAACTACAGTACAGTCAACATCAAACGGTCGTTTGAATAACACCAGTGAAAAATCTGCTGTTGGTCTCCCACCACTCT
CTGAAGCTCCTGCCAACCCCATCCCTCCACCATTGCCCACAGCCCGTCTTCCTGTTTCACATGCTCCTCGGCGTGTACGT
TCCAACCGCAGTTCTCGCAGCACTGCAGAAGGACCTGGAACCCCAGATCCAGATGGTGACAGTTTTAGTCAAAACAGTAG
AATCTTCGAGAGCCAGCAGGGTAAACATACTTTGAAAATGATAGCCTCGATAACAATTCCAATTAAGTATTCGAAGCTCA
TGGGGAAAAATTATTTGATGCCTGATAAGTTCAAATATGAAATTGTGAAATGCAAAGCAAAGAGCCAAGAGTACAGTATT
GAGATCACCGAGAAACAGAAAACAGATCCTGAAAGATGCGGTAAAGGTGCAAAGCTGAATTCCGGGGAAGAAGTTGAAAA
GCTTTGCACTGCCTCTGGGAAGACTTGTTCAACA

Alignment

ORF - retro_ecab_1092 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.54 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKIPKNDPPNEVHTFNFYLSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRE
          IKIP.N..P..V..FNF.LSNV.KDN.Q...D..QQT.S....SQL..L....DK.T.C.T....Q.T..
Retrocopy IKIPPNNSPTDVSNFNFQLSNVSKDNHQ---DHTQQTVSGYSPSQLSWLHLRRDKMTQCRTTNASQITPV

Parental  RMTQAEEESRNRSTKVIKPGGPYVGKRVQIRKAPQAVSDAVPERKRSTPMNPANTIRKTHGSSSVSQRPY
          R.TQAEEES.N...K..KP.G....KR..IRKAPQA..D.VPERKR..P.NPA.TIRK.....SV..RPY
Retrocopy R-TQAEEESCNKWKKIGKPCGK---KRMPIRKAPQAIPDPVPERKRTAPLNPAYTIRKSRVPNSVRLRPY

Parental  RDRVIHLLALKAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNPKDLSYTLKDYVFKELQRDWPGYN
          RDRVIHLLALK.YKK.ELL.RL.KDGV.Q.D.NSL..IL.QVANLN..D.SYTLKDYVFKELQRDWPGY.
Retrocopy RDRVIHLLALKDYKKTELLFRLRKDGVEQNDENSLENILNQVANLNTQDFSYTLKDYVFKELQRDWPGYS

Parental  EIDRRSLESVLSRKLNPSQNAASTSRSESPVCSSRDTASSPQKRLLDSDFIDPLMNKKARISHLTNRVPP
          E.D..SLE.VLS....P.QNA.....SES...SS....SSPQK.L..S..IDPL..KK.RISHLT..V..
Retrocopy ELDKQSLELVLSQRVDPFQNATDINHSESSIGSSTNETSSPQKWLFNSAVIDPLKKKKVRISHLTTTVQS

Parental  TLNGHLNPTSEKSATGLPPPPAAAAISTPPPPPSAHLPVSNPPQTVNSNSNSPSTPEGRGTQDLPVDSFS
          T.NG.LN.TSEKSA.GLPP...A.A...PPP.P.A.LPVS..P..V.SN..S.ST.EG.GT.D...DSFS
Retrocopy TSNGRLNNTSEKSAVGLPPLSEAPANPIPPPLPTARLPVSHAPRRVRSNRSSRSTAEGPGTPDPDGDSFS

Parental  QNGSVYEDQQDKYTSRTSLETLPPGSVLLKCPKPMEENHSMSHKKSKKKSKKHREKDQIKKHDIEMIEEK
          QN....E.QQ.K.T....L..........K..K.M..N..M...K.K....K...K.Q.....IE..E..
Retrocopy QNSRIFESQQGKHT----LKMIASITIPIKYSKLMGKNYLMP-DKFKYEIVKCKAKSQ--EYSIEITEKQ

Parental  EEDLKREEEIAKLNDSSPDSNEGVKEGCTAST
          ..D..R....AKLN............G.T.ST
Retrocopy KTDPERCGKGAKLNSGEEVEKLCTASGKTCST

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	35.48 RPM
SRP021940_cerebellum	0.00 RPM	6.18 RPM
SRP021940_embryo	0.00 RPM	4.19 RPM
SRP021940_placental_villous	0.00 RPM	13.18 RPM
SRP021940_synovial_membrane	0.00 RPM	12.88 RPM
SRP021940_testis	2.88 RPM	17.39 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1092 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010607	1 retrocopy	retro_amel_651,
Dasypus novemcinctus	ENSDNOG00000005103	1 retrocopy	retro_dnov_1413,
Equus caballus	ENSECAG00000022933	1 retrocopy	retro_ecab_1092 ,
Homo sapiens	ENSG00000118985	1 retrocopy	retro_hsap_459,
Nomascus leucogenys	ENSNLEG00000014192	1 retrocopy	retro_nleu_881,
Pongo abelii	ENSPPYG00000015647	1 retrocopy	retro_pabe_1757,
Pan troglodytes	ENSPTRG00000017090	1 retrocopy	retro_ptro_346,