RetrogeneDB ID: retro_pabe_770

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:69363508..69364410(-)
• Located in intron of: None

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_770
AGATCTGCTTCTTCTCTGAGTATGGAGAAGGCAAAAGGCAGGGAGTGGACCTCCTCAGAGAAGTCGAGGGAAGAGGATCA
GCAGGCTTCTAATCAACCAAACACAATTGCTTTGCCAGGAACATCAGCAAAGGGAACCAAAGGAGAAATTTCTGCTAAAG
GTGAAAAAGCGCTCTGCCCAAAGAAGGCGGCAGAGTATAGGGACAACCCCAAACCTCAGAAGAAGATACTAATCCCTTCA
TTACCCTCTAAACCACCACCTGTTAATCGGATTCACCGGGACAGTCTGTGAGCCTGGTGCCTATAATTAAAGACAAAGCC
ACACAGGCCTTTGGTGCCAGAAATAAGCTCCTATGTGCCTTTGCCTGTCCAAATCAAAAGGATTTTCCTAGCACAGCAAA
ACAGGCCAGAATCCAGAAATCATTACCAAAAAAATCAAAGGTGGACAAAGGGGAAATATCCCTGCAAAGCCCTGAGGAGA
CACATCCTTCTGAAGTGGCTCTTCCCCCTGGGGAGGGGTTGCCTGTCCTAGAAGAGTCTGCTGCTCTCCTTGAGGGAGTT
AATACAGTTGTGGTGACAACTTCTGCCCCAGAAGCTTCACTGGCCTCCTGGGCCAGAAATGCAGCCAGGGAGAAGGCACC
AGAAGCAGTGGGATCTCCACATGAGGCCCATGGTGTCAGGTGGCTAGTGTCAGGGAGAAGTCTCCCTGCAGTCACAGATG
GTTGGGTTCACCTCCAGTTTCATGCTAGACAAGCCTGGGTTCCAGAAAATCAAGAAGGGACAGTGAGTGCACTCTTTTTG
CTTCCTGCCTCCAATTCTCTACCCCCATACCTTGAAGACAATATGTTATACCCCAAATGCATTCACAGGTACAAGGTCTT
AATAAAAAGCCTCCAGTGGGAA

Alignment

ORF - retro_pabe_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGSASASMEKAKGKEWTSTEKSREEDQQASNEPNTIALPGTSAKRTKEKMSVKGNKVLCPKKKAEHTDNP
          R...S.SMEKAKG.EWTS.EKSREEDQQASN.PNTIALPGTSAK.TK...S.KG.K.LCPKK.AE..DNP
Retrocopy RSASSLSMEKAKGREWTSSEKSREEDQQASNQPNTIALPGTSAKGTKGEISAKGEKALCPKKAAEYRDNP

Parental  RPQKKIPIPPLPSKLPPVNLIHRDILRAWCQQLKLSSKGQKLDAYKRLCAFAYPNQKDFPSTAKEAKIRK
          .PQKKI.IP.LPSK.PPVN.IHRD.L.AWC..LK........................F.........R.
Retrocopy KPQKKILIPSLPSKPPPVNRIHRDSL*AWCL*LKTKPHRPLVPEISSYVPLPVQIKRIFLAQQNRPESRN

Parental  SLQKKLKVEKG-ETSLQS-SQTHPSEVALPPAGGPPALEDSTPLLEGVNTVVVTTSAPEALLASWARISA
          ..QK.....KG.E.SLQS...THPSEVALPP..G.P.LE.S..LLEGVNTVVVTTSAPEA.LASWAR..A
Retrocopy HYQKNQRWTKG<EISLQSPEETHPSEVALPPGEGLPVLEESAALLEGVNTVVVTTSAPEASLASWARNAA

Parental  RARTPEAVESPQEASGVRWCVVHGKSLPADTDGWVHLQFHAGQAWVPEKQEGRVSALFLLPASNFPPPHL
          R...PEAV.SP.EA.GVRW..V.G.SLPA.TDGWVHLQFHA.QAWVPE.QEG.VSALFLLPASN..PP.L
Retrocopy REKAPEAVGSPHEAHGVRW-LVSGRSLPAVTDGWVHLQFHARQAWVPENQEGTVSALFLLPASNSLPPYL

Parental  EDNMLCPKCVHRNKVLIKSLQWE
          EDNML.PKC.HR.KVLIKSLQWE
Retrocopy EDNMLYPKCIHRYKVLIKSLQWE

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	0.12 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.03 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_770 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_770 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_893
Pan troglodytes	retro_ptro_616
Gorilla gorilla	retro_ggor_723

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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,