RetrogeneDB ID: retro_ptro_2373

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:101087213..101088148(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSPTRG00000006467
• Aliases: None
• Description: None

Sequence

>retro_ptro_2373
AGTCTGGTTGTGATAGGAGCCCCGTTCTTGTAGGGACAGAAAAGAAAAGGAGTGGAACATGGTCCAGCTGCCAGAAGAAA
AATTGGATTGATGAAAAGAGTCTCCAATTTGGGCTGCTGCCTGAAAGACTTTGCAAAGTTTAGTTTTACTCCAGTCCCCA
CAGATGAGCTCTTCAACAACCCTACAGTGAATCTGCGCTCAGTGGCCCAGCCAACCAGCAACTGGCTGAGTTGGTTAGCA
GAGCAGTGTTGTCTGGCTACAGCTGCGTCACGGTGAGAGAAGACCCCAGCCTGGCAATTAGTACCATTAGTGGTCATGCC
TGGAACTGCCCAGACCTTTGTGTCACTTGGGTTGATGCCCAGCAGACATCAGTACACTCCTTACCACTTCATCAGGAAAT
CTCCATGGACTATCTGTTTCATTTCTCCTCAGAGAACTACAGGGAAAGGTACCAGAACTTCCAGGATTTCCCTGGACAAA
CCTTATATCTCTTCCCCAAGTATAGCATATTCTGATCTAGGAGACATGGACCCTCTGGAATATTTTTTTAAAAGAACAAT
GATATCTAGTATTTTTCCATGAGAGACATTGATCCATTTGGCACCCAGGAGGTCATGCAACAGAAATTTGATCTGCTGAT
TGGCAAAAGACAAAGGTCTGTCCATCTGAGTTTTGATATTGATGTATTTGACTGTACACTGGCTCCAGCCGCAGGAATCC
CTATTGTAGGGGGACTGACCTTTCAAGAAGGCATCTATATTACTGAGGAAATACATAGTACAGGGTTGCTGTCAGCACTG
GATCTTGTTGAAGTCAATCCTCAACTGGGCACTTTAGAGGAAAGGGCAAAGGCCACAGCTAGCCTGCCAGTAGATGTAAC
TGCTTTATGTTTGGGTCAGACAAGGGAAGGAGGGCACATTGCCCATGGCCAGATT

Alignment

ORF - retro_ptro_2373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• Parental protein coverage: 88.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSV-G
          S..VIGAPF..GQKRKGVEHGPAA.R..GLMKR.S.LGC.LKDF...SFTPVP.D.L.NN..VN.RSV.G
Retrocopy SLVVIGAPFL*GQKRKGVEHGPAARRKIGLMKRVSNLGCCLKDFAKFSFTPVPTDELFNNPTVNLRSV<G

Parental  LANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAH-ADINTPLTTSSGNLHGQ
          .ANQ.LAE.VSRAV..GYSCVT...D.SLAI.TISGHA..CPDLCV.WVDA..ADI.T.LTTSSGNLHG.
Retrocopy PANQQLAELVSRAVLSGYSCVTVREDPSLAISTISGHAWNCPDLCVTWVDAQ<ADISTLLTTSSGNLHGL

Parental  PVSFLLRELQDKVPQLPGFSWI-KPCISSASIVYIGLRDVDPPEHFIL-KNYDIQYFSMRDIDRLGIQKV
          .VSFLLRELQ.KVP.LPGF.W..KP.ISS.SI.Y..L.D.DP.E.F...KN.DI.YFSMRDID..G.Q.V
Retrocopy SVSFLLRELQGKVPELPGFPWT<KPYISSPSIAYSDLGDMDPLEYFFK<KNNDI*YFSMRDIDPFGTQEV

Parental  MERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQ
          M...FDLLIGKRQR..HLSFDID.FD.TLAPA.G.P.VGGLT..EG.YI.EEIH.TGLLSALDLVEVNPQ
Retrocopy MQQKFDLLIGKRQRSVHLSFDIDVFDCTLAPAAGIPIVGGLTFQEGIYITEEIHSTGLLSALDLVEVNPQ

Parental  LATSEEEAKTTANLAVDVIASSFGQTREGGHIVYDQL
          L.T.EE.AK.TA.L.VDV.A...GQTREGGHI...Q.
Retrocopy LGTLEERAKATASLPVDVTALCLGQTREGGHIAHGQI

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	22.97 RPM
SRP007412_cerebellum	0.00 RPM	18.35 RPM
SRP007412_heart	0.00 RPM	2.54 RPM
SRP007412_kidney	0.00 RPM	22.05 RPM
SRP007412_liver	0.00 RPM	2.82 RPM
SRP007412_testis	0.00 RPM	7.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2373 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2373 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3501
Gorilla gorilla	retro_ggor_2367
Pongo abelii	retro_pabe_2893
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 ,