RetrogeneDB ID: retro_pabe_2349

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:136918663..136919312(-)
• Located in intron of: ENSPPYG00000014122

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA4
• Ensembl ID: ENSPPYG00000013565
• Aliases: None
• Description: developmental pluripotency associated 4 [Source:HGNC Symbol;Acc:19200]

Sequence

>retro_pabe_2349
AGTATGGAGAAGTCAAAAAGGCAAAGAGTGGAAATCCACAGAGAAGTCAAGGGAAGAGGATCAGCAAACTTCTAATTAAC
CAAGCACAACTGCTTTGCCAGGAACATCAGCAAAGAGGACCAAATGAAAAGGTGACAAAGTGCTCTGCCCAAAGAGGAAG
GCAGAGTTCAGCGACAACAACCTAAAACCTCAGAAGAAGATACCAATCCCTCCATTACCCTCTAAACTGCTACCCGTTAA
CCTGATTCGCCAGGACATTCTGTGTGCCTGGTGCCAACAATTAAAGCTGAGCACCAAAGGCCAGAAATTAGATGCACATA
AGCACCCGTGTGCCTTCACCTACCCAAAACAAAAGGACATTCCTAGCACAGCAAAAGAGGCCAGAATTCAGAAATCATTA
CCAAAAAAAAAATCAAAGGTGGACAAGGGGTAAACGTCCCTGAAAAGTTCTGAGGAGACATCCTCCTGAGGTGGCTCTTC
CCTCCTGGGGGGGTGCTGCCTGCCTTGGAAGAGTCTGCTGCTCTCCTTGAAGGAGTTAATACGGCTGTAAGAAAACTTCT
ACCCCAGGTGCTTTGCTGGCCTCCAGGGCCAGAACTGCAGCCAGGGTGGGACACCAGAGGCAGAGGAATCACCACAAGAG
ACCATGGGA

Alignment

ORF - retro_pabe_2349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.44 %
• Parental protein coverage: 71.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SMEKAK-GKEWTSTEKSREEDQQASNEPNTIALPGTSAKRTKEKMSVKGNKVLCPKKKAEHTDNP-RPQK
          SMEK.K.GKEW....KS.E............................KG.KVLCPK.KAE..DN...PQK
Retrocopy SMEKSK>GKEW----KSTEKSREEDQQTSN*PSTTALPGTSAKRTK*KGDKVLCPKRKAEFSDNNLKPQK

Parental  KIPIPPLPSKLPPVNLIHRDILRAWCQQLKLSSKGQKLDAYKRLCAFAYPNQKDFPSTAKEAKIRKSLQK
          KIPIPPLPSKL.PVNLI..DIL.AWCQQLKLS.KGQKLDA.K..CAF.YP.QKD.PSTAKEA.I.KSL..
Retrocopy KIPIPPLPSKLLPVNLIRQDILCAWCQQLKLSTKGQKLDAHKHPCAFTYPKQKDIPSTAKEARIQKSLXX

Parental  KL-KVEKGETSLQSSQ-THPSEVAL-PPAGGPPALEDSTPLLEGVNTVV-VTTSAPEALLASWARISAR-
          ...KV.KG.TSL.SS...HP.EVAL.PP.G..PALE.S..LLEGVNT.V...TS.P.ALLAS.AR..AR.
Retrocopy XXSKVDKG*TSLKSSE>RHPPEVAL>PPGGVLPALEESAALLEGVNTAV<KKTSTPGALLASRARTAAR<

Parental  ARTPEAVESPQEASG
          ..TPEA.ESPQE..G
Retrocopy GGTPEAEESPQETMG

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2349 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2349 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1923
Gorilla gorilla	retro_ggor_1970

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349 , retro_pabe_770,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,