RetrogeneDB ID: retro_ptro_2542

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:64209563..64209980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM162B
• Ensembl ID: ENSPTRG00000018538
• Aliases: None
• Description: family with sequence similarity 162, member B [Source:HGNC Symbol;Acc:21549]

Sequence

>retro_ptro_2542
TGTGCCCCTGGGAAGCCTCTAGAAGCCACACAGAGGCCCATAGCAACTCTCATGCCCTGGAGGGTCTCACCAGCCACTCC
AGTGATGGGCCCTCCAGTAGCTCTGGGACCCAAGCAGGGATGATTCACAAAGTCCCTACCAAGCACAGGCCTTCACAGTT
CAACAAGAAAATCCTACTGTTGACTGGATTTTTAAAAATCAGTGGAGGAGATCACACTAGAAATGATAGATACTGCAAGA
AACAAAGCTTGAGTGAAAGCTTGTTACCGTAATGAATGGACTCACACATATCACTGCTTTGCAGTGATAGCATCAGCCAA
AAAGGCTGCAGAACATGAATCATTAACAAGTTGAAATATGTCAAAGATGGCTGTGTGGTGTGAAGAAGCTGCATTAGCTG
CACAGGCTAAGCCTAAA

Alignment

ORF - retro_ptro_2542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.43 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CGPGAPLEATRRP-APALPPR-GLPCYSSGGAPSNSGPQGHGEIHRVPTQRRPSQFDKKILLWTGRFK-S
          C.PG.PLEAT.RP.A...P.R.GL...SS.G..S.SG.Q..G.IH.VPT..RPSQF.KKILL.TG..K.S
Retrocopy CAPGKPLEATQRPIATLMPWR<GLTSHSSDGPSSSSGTQA-GMIHKVPTKHRPSQFNKKILLLTGFLK>S

Parental  MEEIPPRIPPEMIDTARNKARVKACY-IMIGLTIIA-CFAVIVSAKRAVERHESLTSWNLAKKAKWREEA
          .EE....I..EMIDTARNKA.VKACY..M.GLT.I..CFAVI.SAK.A.E.HESLTS.N..K.A.W.EEA
Retrocopy VEE----ITLEMIDTARNKA*VKACY>VMNGLTHIT<CFAVIASAKKAAE-HESLTS*NMSKMAVWCEEA

Parental  ALAAQAKAK
          ALAAQAK.K
Retrocopy ALAAQAKPK

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	0.05 RPM	1.34 RPM
SRP007412_cerebellum	0.00 RPM	0.25 RPM
SRP007412_heart	0.00 RPM	2.48 RPM
SRP007412_kidney	0.00 RPM	3.01 RPM
SRP007412_liver	0.00 RPM	0.72 RPM
SRP007412_testis	0.00 RPM	1.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2542 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2542 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3744
Pan troglodytes	retro_ptro_2994
Pan troglodytes	retro_ptro_2541

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183807	2 retrocopies	retro_hsap_3744, retro_hsap_901,
Gorilla gorilla	ENSGGOG00000002045	1 retrocopy	retro_ggor_728,
Microcebus murinus	ENSMICG00000014555	1 retrocopy	retro_mmur_746,
Mus musculus	ENSMUSG00000019909	1 retrocopy	retro_mmus_2292,
Pan troglodytes	ENSPTRG00000018538	4 retrocopies	retro_ptro_2541, retro_ptro_2542 , retro_ptro_2994, retro_ptro_621,