RetrogeneDB ID: retro_pabe_2310

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:67771652..67772080(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000013705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSPPYG00000019082
• Aliases: None
• Description: histidine triad nucleotide binding protein 2 [Source:HGNC Symbol;Acc:18344]

Sequence

>retro_pabe_2310
AGAGCCATGGCGGCCACAGGGCTGCGCAGCACACACATCTGAGGAGCTGTAGGTGTGACTGGTGGGAATGAAATGACCAA
GGCCCAGCGGGCACTTCCTGGGGGTGTAGCCCCAACCATCTTCTGTGGGATCCTGGACCATCGCCTCCCAGCCTACATTC
TATATGAGGACTAGCAGTGTCTTGTGTTCCCTGATGTGGCTCCGTAGGCTCCTGTGCACTTTCTGGTCATTCCTAAGAAG
CCCATTCCTCGGATTAACCAGGCTGAACAAGAAGACAGCAGCTTCTTGGACACCTACTCCTTGTGTCTAAGAAGATAGCA
AGGGCTGAGGGCCTAGGAGATGGATACCGACTTGTGATCAATGATGAACAATCTGTAAATTACCTGCACATTCACTTACT
TGGGAGCTGACAGCTCCAGTGGCCTCCA

Alignment

ORF - retro_pabe_2310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 90.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAVAATGARGGQVRGAAGVTDGNEVAKSQQATPGGAAPTIFSRILDRSLPADILYEDQQCLVFRDVAPQA
          .A.AATG.R.....GA.GVT.GNE..K.Q.A.PGG.APTIF..ILD..LPA.ILYED.QCLVF.DVAP.A
Retrocopy RAMAATGLRSTHI*GAVGVTGGNEMTKAQRALPGGVAPTIFCGILDHRLPAYILYED*QCLVFPDVAP*A

Parental  PVHFLVIPKKPIPRISQAEEED-QQLLGHLLLVAKKTAKAEGLGDGYRLVINDGKLGAQSVYHLHIHVLG
          PVHFLVIPKKPIPRI.QAE.ED.QQLLGHLLLV.KK.A.AEGLGDGYRLVIND.....QSV..LHIH.LG
Retrocopy PVHFLVIPKKPIPRINQAEQED<QQLLGHLLLVSKKIARAEGLGDGYRLVIND----EQSVNYLHIHLLG

Parental  GRQLQWPP
          ..QLQWPP
Retrocopy S*QLQWPP

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	13.10 RPM
SRP007412_cerebellum	0.00 RPM	8.76 RPM
SRP007412_heart	0.06 RPM	8.94 RPM
SRP007412_kidney	0.03 RPM	55.06 RPM
SRP007412_liver	0.00 RPM	14.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2310 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2310 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2603
Pan troglodytes	retro_ptro_1754
Gorilla gorilla	retro_ggor_1823
Macaca mulatta	retro_mmul_1509
Callithrix jacchus	retro_cjac_1343

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201, retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000015747	2 retrocopies	retro_pabe_3189, retro_pabe_909,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310 ,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,