RetrogeneDB ID: retro_pabe_1567

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:69785272..69785934(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOD1
• Ensembl ID: ENSPPYG00000016057
• Aliases: None
• Description: biorientation of chromosomes in cell division 1 [Source:HGNC Symbol;Acc:25114]

Sequence

>retro_pabe_1567
TCACCTCTGCCGCTGCCTCCTTGGGGCCCTCCTCCTTCACCGCCCCCTTAGCCACCTCTACACATTCTAGGCCTTCTGTC
CTGGAGAAGAAGCTATAATCGGTCTCCCTGTGGGTCCGGTGCGCAGCCATGGCGGACGGCGGCGGCGGCAGCTGCGGTGC
GGGCCAGGCCTCGGCCGGAGCAGCCACGGGCGCGACCCGGGCCAGCGGGGGCGGCGGCCCCATCAACCCGGCCTCGTTGC
CCCCTGGCGACCCTCAGCTCATCGCTGTCATCGTGGGGCAGCTCAAGAGCCGGGGCCTTTTTGACAGCTTCCGCCGGGAC
TGCAAGGCTGACGCGGACACCAAGCCAGCTTACCAAAACCTGAGCCAGAAAGCAGATAATTTTGTGTCGACACATCTGGA
CAAGCAGGAATGGAATCCTCCAACGAACGAAAACCAACTGCGCTATGGTCTGAGGCAGAGTGTGGTTCAGTCAGGGAGGT
CAGAAGCTGGAGTGGACAGGATTGGTTCTCAGGTGGTGGATCCAAAACTAAACCACATCTTCAGGCCACAAATAGAACAA
ATAATTCATGAATTCCTGGTGGCCCAGAAAGAAGCAGCTGTGCCAGCACTCCCTCCAGAGCCGGAAGGCCAGGACCCTCC
AGCTCCGTCTCAGGACACTTCC

Alignment

ORF - retro_pabe_1567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.91 %
• Parental protein coverage: 80.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPPPLPPWGPPPSPPPSPPLHVLGLLSWRRSYSRSP-LWARGAAMADGGGGGGTGAVGGGGTGQASAGAA
          SP.PLPPWGPPPSPPP.PPLH.LGLLSWRRSY.RSP.LW.R.AAMADGGGG......G.G......A..A
Retrocopy SPLPLPPWGPPPSPPP*PPLHILGLLSWRRSYNRSP<LWVRCAAMADGGGG----SCGAGQASAGAATGA

Parental  TGATGASGGGGSINPASLPPGDPQLIALIVEQLKSRGLFDSFRRDCLADVDTKPAYQNLRQKVDNFVSTH
          T.A.G...GGG.INPASLPPGDPQLIA.IV.QLKSRGLFDSFRRDC.AD.DTKPAYQNL.QK.DNFVSTH
Retrocopy TRASG---GGGPINPASLPPGDPQLIAVIVGQLKSRGLFDSFRRDCKADADTKPAYQNLSQKADNFVSTH

Parental  LDKQEWNPTMNKNQLRNGLRQSVVQSGMLEAGVDRIISQVVDPKLNHIFRPQIERAIHEFLAAQKKAAVP
          LDKQEWNP..N.NQLR.GLRQSVVQSG..EAGVDRI.SQVVDPKLNHIFRPQIE..IHEFL.AQK.AAVP
Retrocopy LDKQEWNPPTNENQLRYGLRQSVVQSGRSEAGVDRIGSQVVDPKLNHIFRPQIEQIIHEFLVAQKEAAVP

Parental  APPPEPEGQDPPAPSQDTS
          A.PPEPEGQDPPAPSQDTS
Retrocopy ALPPEPEGQDPPAPSQDTS

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	30.80 RPM
SRP007412_cerebellum	0.00 RPM	40.74 RPM
SRP007412_heart	0.00 RPM	12.46 RPM
SRP007412_kidney	0.00 RPM	18.50 RPM
SRP007412_liver	0.00 RPM	15.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1567 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1567 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1567 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_102

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567 , retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,