RetrogeneDB ID: retro_ecab_981

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:83178973..83179964(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSECAG00000000554
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_ecab_981
AGGCTGAGGAAATTTCAGTACTGAGGCAAAGAAGCATCTACGAGGCAGCAACAGCAGATGGCAATCAGCCTACAGCTCCA
GAAAGCCAAGAAAGACGAGCAGGCTGTAAAGAGAAGGAACATGACCAATCTCTCACCTGACTCAGTTTCAGGAAAGCTCA
CCAAATTGGTCAGCTTCCCCCTGCATGAAATAATCAATGGTGTGACTCCTCGGACCCAGAGCTATGTGTCCAGGCCACTC
AGGCAGCCAGGAAAATGCTGTCTCAAGAAAGAAGCCCTCCTCTAAAATAGATTGTTGAAGCAAGGCTCGTTCTCATGCTG
CTGGAGCTCCTGAAGTCATGGCTTCACCACTGCTTGCGGTTGAGGCAGCCTGGGCTCTGACCAGCACAGCTTCATTGACT
TTGGAGCAGACACCAGCTGTTGTGGACGGAGTGCCATCCAGCCCTTGAGTGAGCTTCTGTCTTCCCCTGGTGTGACTGTT
TGTGAACAGGTAATGTGGGTTCTTGGTAACAGAGCAGGTGACAGCTGAGAATTCAGAGACATCGTCCTCTTGAGCAATGC
TGTCCCACATCTGCTGGCCCTGGTTTTTCATCAACCATACCCATCCCATTTCTGTAGAACATCATGTGGACCTTGTCCAC
ACTGGAGCAAAACAACAACCGGTACTCTTGTGAAAAAGTGGTCAAGTAAATGTTGTTACTCCTCTTCCACCTCCCACAGC
GTCGTGGCAATGAGGTTCCCTGGGACACCTGCTGGGCCATGTCCTACCTCATGATGGCTGCAATGAGTGCATCTGCCAAA
CGGTTGACAAGGGGGTCCTGTCTGGCTGCTAGAGCTCATGACCAGTTTGAGGCTCAATGTCTTGACCCCCTCTCTCCACA
CTGTGGAAACTTCGTCATTGTAACGGATCACCAGAACTAAGTGGCCGTTGACACAGGCGGCTGAGCATGCTGCCCCAGCT
CCTGATGCACCGCAAGTTCTCCATCCAGAGG

Alignment

ORF - retro_ecab_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.76 %
• Parental protein coverage: 68.45 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  RLRKFKYRGKDTAVRRQQRIAVSLELRKAKKDEQALKRRNITPLSPDPASEQQTKAINLTLQEIINGV-N
          RLRKF.Y.GK....R.QQ..A.SL.L.KAKKDEQA.KRRN.T.LSPD..S...TK.....L.EIINGV..
Retrocopy RLRKFQY*GKEASTRQQQQMAISLQLQKAKKDEQAVKRRNMTNLSPDSVSGKLTKLVSFPLHEIINGV<D

Parental  ASDPDLCFQATQAARKMLSRERNPPLKLIIEAGLIPRLVEFLKSSLHPCLQF-EAAWALTNIASGTSEQT
          .SDP.LC.QATQAARKMLS.ER.PPLK.I.EA.L...L.E.LKS.LH.CL...EAAWALT..AS.T.EQT
Retrocopy SSDPELCVQATQAARKMLSQERSPPLK*IVEARLVLMLLELLKSWLHHCLRL<EAAWALTSTASLTLEQT

Parental  RAVVEG-GAIQPLVELLSSPHMTVCEQAVWALGNIAGDGPEFRDIVISSNVIPQLRALI-SSTT-PITFL
          .AVV.G..AIQPL.ELLSSP..TVCEQ..W.LGN.AGD..EFRDIV..SN..P.L.AL...S.T.PI.FL
Retrocopy PAVVDG<SAIQPLSELLSSPGVTVCEQVMWVLGNRAGDS*EFRDIVLLSNAVPHLLALV<FSSTIPIPFL

Parental  RNITWTLSNLCRNKNPYPCERAVKQMLPVLSRLLQHQDSEVLSDACWALSYLT-DGCNDRIGQVVDIGVL
          .NI.WTLS.L..N.N.Y.CE..VK.ML..L..L.Q....EV..D.CWA.SYL..DGCN..I.Q.VD.GVL
Retrocopy *NIMWTLSTLEQNNNRYSCEKVVK*MLLLLFHLPQRRGNEVPWDTCWAMSYLM<DGCNECICQTVDKGVL

Parental  PR-LVELMTSSELNVLTPSLRTV-GNVVTGTDHQTQVAIDAG-MLSVLPQLLMHPKASIQK
          ...L.ELMTS..LNVLTPSL.TV.GN.V..TDHQ..VA.D.G..LS.LPQLLMH.K.SIQ.
Retrocopy SG<LLELMTSLRLNVLTPSLHTV<GNFVIVTDHQN*VAVDTG<RLSMLPQLLMHRKFSIQR

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.10 RPM	0.05 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.36 RPM	0.05 RPM
SRP021940_testis	0.00 RPM	1.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_981 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981 ,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,