RetrogeneDB ID: retro_ptro_106

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:20698081..20698939(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000006940
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM92B
• Ensembl ID: ENSPTRG00000008427
• Aliases: None
• Description: family with sequence similarity 92, member B [Source:HGNC Symbol;Acc:24781]

Sequence

>retro_ptro_106
CGGGAGACGCTGGGTCGGAACGCTCAAACGAAACAACTGCAAACAGCTGTCTCAAATGTGGAGAAGCATTTTGGAGAACT
GTGCCAAATCTTCGCTGCCTATGTGCGGAAAACTGCCAGGCTGAGAGACAAAGCAGACCTCCTGGTGAATGAAATTAACG
CGTATGCTGCTACAGAGACCCCGCATTTAAAGCTGGGCCTGATGAACTTTGCAGATGAGTTTGCCAAACTTCAGGATTAT
CGACAAGCAGAGGTTGAAAGACTTGAAGCCAAAGTAGTTGAACCCTTGAAAACTTATGGGACCATTGTGAAAATGAAACG
GGATGACCTCAAAGCAACACTCACAGCAAGGAATCGAGAAGCTAAGCAATTAACTCAGTTAGAAAGAACACGTCAGCGAA
ACCCATCTGATCGACATGTTATTTCACAGGCAGAAACGGAATTACAGAGAGCTGCAATGGATGCTAGCCGAACAAGTCGT
CATCTGGAGGAAACTATTAACAACGTTGAAACGCAGAAAATGAAGGATATAAAGACTATATTTTCTGAATTTATCACAAT
CGAAATGTTATTTCACGGCAAAGCTTTAGAGGTCTACACTGCTGCCTACCAGAATATACAAAACATTGACGAAGATGAAG
ATTTAGAGGTTTTCCGAAATTCTCTGTATGCACCAGATCATTCATCTCGTTTAGATATTGTAAGAGCAAATTCAAAGTCA
CCTCTTCAGAGATCACTGTCAGCTAAGTGTGTATCTGGAACAGGACAGGTATCCACTTGTCGACTAAGAAAGGATCAACA
AGCAGAAGATGATGAGGATGAAGAGTTAGATGTTACAGAAGAAGAAAATTTTCTTAAG

Alignment

ORF - retro_ptro_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.93 %
• Parental protein coverage: 70.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDSQVRVMENIVANTEKYFGQFCSLLAAYTRKTARLRDKADQLVKQLIDFANSENPELRATMRGFAEDLA
          R..Q.......V.N.EK.FG..C...AAY.RKTARLRDKAD.LV......A..E.P.L......FA...A
Retrocopy RNAQTKQLQTAVSNVEKHFGELCQIFAAYVRKTARLRDKADLLVNEINAYAATETPHLKLGLMNFADEFA

Parental  KVQDYRQAQVERLETKVVNPLKLYGAQIKQTRAEIKKFKHVQNHEIKQLEKLEKLRQKSPSDQQMIGQAE
          K.QDYRQA.VERLE.KVV.PLK.YG...K..R...K......N.E.KQL..LE..RQ..PSD...I.QAE
Retrocopy KLQDYRQAEVERLEAKVVEPLKTYGTIVKMKRDDLKATLTARNREAKQLTQLERTRQRNPSDRHVISQAE

Parental  TRVQRAAVDSSRTTLHLEETVDAFQRQKLKDLQKFFCDFVTIEMVFHAKAVEVYSSAFQTLEKYDLERDL
          T..QRAA.D.SRT..HLEET......QK.KD....F..F.TIEM.FH.KA.EVY..A.Q.....D...DL
Retrocopy TELQRAAMDASRTSRHLEETINNVETQKMKDIKTIFSEFITIEMLFHGKALEVYTAAYQNIQNIDEDEDL

Parental  LDFR
          ..FR
Retrocopy EVFR

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	5.63 RPM	0.02 RPM
SRP007412_cerebellum	3.87 RPM	0.22 RPM
SRP007412_heart	4.93 RPM	0.00 RPM
SRP007412_kidney	3.98 RPM	0.00 RPM
SRP007412_liver	2.55 RPM	0.00 RPM
SRP007412_testis	70.50 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ptro_106 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EX654481	38071171	38071276	95.3	100	5	95

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008427	1 retrocopy	retro_ptro_106 ,