RetrogeneDB ID: retro_pabe_2323

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:95019963..95020435(-)
• Located in intron of: ENSPPYG00000013832

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA3
• Ensembl ID: ENSPPYG00000004230
• Aliases: None
• Description: developmental pluripotency associated 3 [Source:HGNC Symbol;Acc:19199]

Sequence

>retro_pabe_2323
AAGTTTGATCCGACCTTGGTCCCAGAGTCTTCACAAATGCTCACTGAAGAAAATTCCCAGGACGATTCGGGGGCCTCTCA
AAACTTCTGCTTCAAGACGTTGATAAAGAACCATAGTAACTTGATTATACACCCTAGTACTGAATTCCCTTCCCATCTAC
CAGAAAATTCACCCCAACAACAACATACAGGAGCAATGATGCTCAGGGAAATCAGAGATGACTTGCTCTACATGAGAGGG
GTAAGAACACTGCTGTCTGTGTAGAAAGAAAAGGATGGCAAAATTGAGATACATTTTACTCAGCAGAGTTCCTAGGCTTG
AAAGAGAACTAACAAACACTGGGCTTAAGAGAGTTCAGAATGAATCAAGTAGTGGACCATTCAGATGTCGCTGCAGTTTC
TGCATGTATAACCAATGGGATCCTTCTGAGGATGCTAGAATACGGAATTATGACACTCAGCCACGTCAGCCA

Alignment

ORF - retro_pabe_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.12 %
• Parental protein coverage: 96.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFNPTYIPESPQMLTEENSRDDSGASQ-ICSETLIKHLSNLTINASSQTASPLSEALLRRQSARAAVLKE
          KF.PT..PES.QMLTEENS.DDSGASQ..C..TLIK..SNL.I..S....S.L.E.....Q...A..L.E
Retrocopy KFDPTLVPESSQMLTEENSQDDSGASQNFCFKTLIKNHSNLIIHPSTEFPSHLPENSPQQQHTGAMMLRE

Parental  IEDEWLYSGRGVRTLLSVQREK-MARLRYMLLGRVRTHERIPTNKGPKGVKKESR--PFKCPCSFCVSNG
          I.D..LY..RGVRTLLSV..EK.MA.LRY.LL.RV...ER..TN.G.K.V..ES...PF.C.CSFC..N.
Retrocopy IRDDLLYM-RGVRTLLSV*KEK>MAKLRYILLSRVPRLERELTNTGLKRVQNESSSGPFRCRCSFCMYNQ

Parental  WDPSENARIGNQDTKPLQP
          WDPSE.ARI.N.DT.P.QP
Retrocopy WDPSEDARIRNYDTQPRQP

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	0.00 RPM	0.00 RPM
SRP007412_kidney	0.03 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2323 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2323 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2648
Pan troglodytes	retro_ptro_1783
Gorilla gorilla	retro_ggor_1849
Callithrix jacchus	retro_cjac_1329

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046609	1 retrocopy	retro_btau_1001,
Canis familiaris	ENSCAFG00000032092	1 retrocopy	retro_cfam_1926,
Callithrix jacchus	ENSCJAG00000005409	10 retrocopies	retro_cjac_1329, retro_cjac_1446, retro_cjac_1465, retro_cjac_1474, retro_cjac_2052, retro_cjac_2628, retro_cjac_3162, retro_cjac_4006, retro_cjac_622, retro_cjac_730,
Homo sapiens	ENSG00000187569	6 retrocopies	retro_hsap_1043, retro_hsap_1323, retro_hsap_1618, retro_hsap_2648, retro_hsap_4010, retro_hsap_4887,
Gorilla gorilla	ENSGGOG00000013040	4 retrocopies	retro_ggor_1849, retro_ggor_2693, retro_ggor_3052, retro_ggor_823,
Mustela putorius furo	ENSMPUG00000017530	3 retrocopies	retro_mputfur_1220, retro_mputfur_1452, retro_mputfur_520,
Mus musculus	ENSMUSG00000046323	4 retrocopies	retro_mmus_1186, retro_mmus_1682, retro_mmus_1838, retro_mmus_3598,
Nomascus leucogenys	ENSNLEG00000026887	2 retrocopies	retro_nleu_2041, retro_nleu_914,
Otolemur garnettii	ENSOGAG00000024813	7 retrocopies	retro_ogar_1514, retro_ogar_1618, retro_ogar_1775, retro_ogar_1780, retro_ogar_1964, retro_ogar_2538, retro_ogar_3406,
Pongo abelii	ENSPPYG00000004230	6 retrocopies	retro_pabe_1338, retro_pabe_1962, retro_pabe_2323 , retro_pabe_3586, retro_pabe_873, retro_pabe_975,
Pan troglodytes	ENSPTRG00000004617	7 retrocopies	retro_ptro_1085, retro_ptro_1783, retro_ptro_2701, retro_ptro_2722, retro_ptro_3148, retro_ptro_711, retro_ptro_904,
Rattus norvegicus	ENSRNOG00000022950	4 retrocopies	retro_rnor_1249, retro_rnor_1816, retro_rnor_2234, retro_rnor_395,
Tursiops truncatus	ENSTTRG00000000751	3 retrocopies	retro_ttru_1293, retro_ttru_1911, retro_ttru_84,