RetrogeneDB ID: retro_pabe_2893

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:101738311..101739288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSPPYG00000005926
• Aliases: None
• Description: arginase 2 [Source:HGNC Symbol;Acc:664]

Sequence

>retro_pabe_2893
AAACTTGTCTCCTCCAGACACAAGTGCATTCTGTCCTGAAGAAGTCTGGTTGTGATAGGAGCCCCGTTCTTGTAGGGATA
GAAAAGAAAAGGAGTGGAACATGGTCCAGCTGCCAGAAGAAAAGTTGGATTGATGAAAAGGGTCTCCAATTTGGGCTGCT
GCCTAAAAGACTTTGGAAAGTTTAGTTTTACTCCAGTCCCCACAGATGAGCTCTTCAACAACCCTACAGTGAATCTGTGC
TCAGTGGCCCAGCCAACCAGCAACTGGCTGAGTTGGTTAGCAGAGCAGTGTTGTCTGGCTATAGCTGCGTCACGGTGAGA
TAAGACCCCAGCCTGGCAATTAGTACCATTAGTGGCCATGCCTGGAACTGCCCAGACCTTTGTGTCACTTGGGTTGATGC
CCAGCAGACATCAGTACACCCCTTACCACTTCATCAGGAAATCTCCATGGACTATCAGCTTCTTTTCTCCTCAGAGAACT
ACAGGGAAAGTTACCAGAAGTTCCAGGATTTCCCTGGACAAACCTTGTGTCTCTTCCCCAAGTATAGCGTATTCTGATCT
AGGAGATGTGGACCCTCTGGAACATTTTTTTAAAAGAACAATGATATCTAGTATTTTTCCATGAGAGACATTGATCCATT
TGGCACCCAGAAGGTCATGCAACAGAAATTTGATCTGCTGATTGGCAAAAGACAAAGGTCTGTCCATCTGAGTTTTGATA
TTGATGTATTTGACTCTACACTGGCTCCAGCCACAGGAATCCCTATTGTAGGGGGACTGACCTTTCAAAAAGGCATCTAT
ATTACTGGGGAAATACATAGTACAGGGTTGCTGTCAGCACTGGATCTTGTCGAAGTCAATCCTCAACTGGGCACTTTAGA
GGAAAGGGCAAAGGCCACAGCTAGCCTGCCAGTAGATGTAACTGCTTTATGTTTGGGTCAGACAAGGGAAGGAGGGCACA
TTGCCCATGGCCAGATT

Alignment

ORF - retro_pabe_2893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.47 %
• Parental protein coverage: 92.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RLLQTRVHSILKKSVHSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPK
          .L...R...IL..S..S..VIGAPF..G.KRKGVEHGPAA.R..GLMKR.S.LGC.LKDFG..SFTPVP.
Retrocopy KLVSSRHKCIL--S*RSLVVIGAPFL*G*KRKGVEHGPAARRKVGLMKRVSNLGCCLKDFGKFSFTPVPT

Parental  DDLYNNLIVNPRSV-GLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISEHARHCPDLCVVWVDGH-A
          D.L.NN..VN..SV.G.ANQ.LAE.VSRAV..GYSCVT...D.SLAI.TIS.HA..CPDLCV.WVD...A
Retrocopy DELFNNPTVNLCSV<GPANQQLAELVSRAVLSGYSCVTVR*DPSLAISTISGHAWNCPDLCVTWVDAQ<A

Parental  DINTPLTTSSGNLHH-KVSFLLRELQDKVPQLPGFSWI-KPCISSASIVYIGLRDVDPPEHFIL-KNYDI
          DI.TPLTTSSGNLH....SFLLRELQ.K.P..PGF.W..KPC.SS.SI.Y..L.DVDP.EHF...KN.DI
Retrocopy DISTPLTTSSGNLHGLSASFLLRELQGKLPEVPGFPWT<KPCVSSPSIAYSDLGDVDPLEHFFK<KNNDI

Parental  QYFSMRDIDRLGIQKVMEQTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIH
          .YFSMRDID..G.QKVM.Q.FDLLIGKRQR..HLSFDID.FD.TLAPATG.P.VGGLT...G.YI..EIH
Retrocopy *YFSMRDIDPFGTQKVMQQKFDLLIGKRQRSVHLSFDIDVFDSTLAPATGIPIVGGLTFQKGIYITGEIH

Parental  NTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREGGHIVYDQL
          .TGLLSALDLVEVNPQL.T.EE.AK.TA.L.VDV.A...GQTREGGHI...Q.
Retrocopy STGLLSALDLVEVNPQLGTLEERAKATASLPVDVTALCLGQTREGGHIAHGQI

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.94 RPM
SRP007412_cerebellum	0.00 RPM	19.58 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.00 RPM	14.95 RPM
SRP007412_liver	0.00 RPM	12.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2893 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2893 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2893 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3501
Pan troglodytes	retro_ptro_2373
Gorilla gorilla	retro_ggor_2367
Callithrix jacchus	retro_cjac_2357

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893 ,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,