RetrogeneDB ID: retro_pabe_1345

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:22645874..22646508(+)
• Located in intron of: ENSPPYG00000007189

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000013118
• Aliases: None
• Description: None

Sequence

>retro_pabe_1345
GCAATATATTACAACATAAAGCACGGATATGCAAATAGATCTCTGGCTATTTTTGACAAGCCAATACATCCACTTTCACA
AGAGAAGGTTCCAGGGAAATCCTTCCAGCATGATCCCAAACACAACTGTACTTTCAGATATTTCTGTACTCTTTTTCAAG
TCATAAAACTAACAGCTCCATGTGCAATTGTAGCTTTGGTGTACATTGAACGACTTTTAACTAATGGTAGCATCGCTCTT
TGTCCTACTAATTGGAAAAAGATTGTCCTTGGAGCCATGCTTCTTGCCTCCAAGGTTTGGAGAAATCATGGTCTGTGGTG
TGGATGACAGCCAGAATCCCAAGGACATTGCAGTTGAGAACATGAGCAAGATGGAGAAGTGTTTTTTGGAGCTACTTGAG
TTTAATATTCATGTGTCTGCCAGTGTTTATGCAAGATATTACTTCGACCTGCGTGCCTTGGCAAATGACCGTGACCTGTA
TTTTCTATTTAGTTTTCTTCACAAAGATAAAGCACAGAAACTGGAGGCTGTGTCATGGCCATGTGAATACAAAGACTTGC
ATCAACATGCTGCTGCTATGACAACGGCTAGCAGCATGAATTTCACTGGTAGTCGGTGCACTAATGCCATCTTA

Alignment

ORF - retro_pabe_1345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.46 %
• Parental protein coverage: 73.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AIYYHIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLE
          AIYY.IK...ANRSL.IFD...HPL..EKVP...F.HDP.H....R...TLF....LTA.CAIV.LVY.E
Retrocopy AIYYNIKHGYANRSLAIFDKPIHPLSQEKVPGKSFQHDPKHNCTFRYFCTLFQVIKLTAPCAIVALVYIE

Parental  RLLTYAEIDICPTNW-KRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINV
          RLLT...I..CPTNW.KR..L....L.........V..VD..Q..KDI.VE.M..ME..FLELL.FNI.V
Retrocopy RLLTNGSIALCPTNW>KRLSLEPCFLPPR-FGEIMVCGVDDSQNPKDIAVENMSKMEKCFLELLEFNIHV

Parental  PASVYAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKDLCR-AAMRRSFSADNFIGIQRSK
          .ASVYA.YYFDLR.LA.D..L.FLF..L.K..AQ.LEA.S..CE.KDL...AA.....S..NF.G.....
Retrocopy SASVYARYYFDLRALANDRDLYFLFSFLHKDKAQKLEAVSWPCEYKDLHQHAAAMTTASSMNFTGSRCTN

Parental  AIL
          AIL
Retrocopy AIL

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	0.55 RPM	2.49 RPM
SRP007412_cerebellum	0.49 RPM	1.22 RPM
SRP007412_heart	0.15 RPM	1.69 RPM
SRP007412_kidney	0.33 RPM	2.52 RPM
SRP007412_liver	0.55 RPM	3.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1345 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1345 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1629
Gorilla gorilla	retro_ggor_1229

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164, retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345 , retro_pabe_3766, retro_pabe_76,