RetrogeneDB ID: retro_ptro_3266

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:125888473..125889236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSPTRG00000000208
• Aliases: None
• Description: filamin binding LIM protein 1 [Source:HGNC Symbol;Acc:24686]

Sequence

>retro_ptro_3266
ATGGCCTCAAAGCCTGAGAAGAGTGTGGCATCGTCTGTCTTTATCACCCTTGCACCCCTGTGCCGCGATTTAGCTGTGGT
TGAGGAAGGGAGGCAGGCGGTTTGTGAGGCCTGATGTGGCCTCCCCTGGGAGGCTCCTGCCCCCATGAAGGCACCCGGAG
CTGGCTTAGCGGGAAAGCCCAGCCCCTGGGCACCCCCTGGCAGGGCTGCAGCCACAGTGCCAGCTGCACCTCTGCAGCTC
TCCAATGGAGGATGCTCACCCCCTCCTCCTGTCCTGGATGGTGAGGACGCACTTCCTGACCTGGACCTCGTCCCACCCCC
TCCACTGCCCCCTCCAGTGCTCCTGTCTTCTGAAGAAGAGGCTCCTGCTCCAATGGGGGCCTCACTCATTGCAGACTTAG
AGCAGTTGCACCTGCCCTCGCCCCCACCCCGACCACAGGCCCCAGTGGAGGGACCTTCAGTCCAGCCTGGGCCCAGTCCC
CTCAGGCCTGGGGAGGAAGAGCTTCCGCCTTCCCCAGCAGAGCCTGTTGAGAGAGAGTCGTCCACAGACATCTGTGCCTT
CTGCCACAAAACCGTGTCCTCCCCAAGAGCTGGCTGTGGAGGCCATAAAGAGGCAGTACCATGCCCAGTGCTTCACGTGG
CACACCTGCCACCGCCAGCTAGCTGGGCAGAGCTTCTACCAGGATGGGCGACCCCTCTGCGAACCCTGCTACCAGGACAC
GCTGGAGAAGTGCGGCAAGTGTGGCCAGGTGGTCCGGGAACAC

Alignment

ORF - retro_ptro_3266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.59 %
• Parental protein coverage: 67.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASKPEKRVASSVFITLAPPRRDVAVAEEVRQAVCEARRGRPWEAPAPMKTPEAGLAGRPSPWTTPGRAA
          MASKPEK.VASSVFITLAP..RD.AV.EE.RQAVCEA..G.PWEAPAPMK.P.AGLAG.PSPW..PGRAA
Retrocopy MASKPEKSVASSVFITLAPLCRDLAVVEEGRQAVCEA*CGLPWEAPAPMKAPGAGLAGKPSPWAPPGRAA

Parental  ATVPAAPMQLSNGGCPPPPPVLDGEDVLPDLDLLPPPPPPPPVLLPSEEEAPAPMGASLIADLEQLHLSP
          ATVPAAP.QLSNGGC.PPPPVLDGED.LPDLDL.PPPP.PPPVLL.SEEEAPAPMGASLIADLEQLHL..
Retrocopy ATVPAAPLQLSNGGCSPPPPVLDGEDALPDLDLVPPPPLPPPVLLSSEEEAPAPMGASLIADLEQLHLPS

Parental  PPPPPQAPAEGPSVQ--PCPLRPVEEELPPPPAEPVEKGASTDICAFCHKTVS-PRELAVEAMKRQYHAQ
          PPP.PQAP.EGPSVQ..P.PLRP.EEELPP.PAEPVE...STDICAFCHKTVS.P.ELAVEA.KRQYHAQ
Retrocopy PPPRPQAPVEGPSVQPGPSPLRPGEEELPPSPAEPVERESSTDICAFCHKTVS>PQELAVEAIKRQYHAQ

Parental  CFTCRTCRRQLAGQSFYQKDGRPLCEPCYQDTLERCGKCGEVVRDH
          CFT..TC.RQLAGQSFYQ.DGRPLCEPCYQDTLE.CGKCG.VVR.H
Retrocopy CFTWHTCHRQLAGQSFYQ-DGRPLCEPCYQDTLEKCGKCGQVVREH

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	0.79 RPM
SRP007412_cerebellum	0.00 RPM	3.30 RPM
SRP007412_heart	0.00 RPM	10.49 RPM
SRP007412_kidney	0.00 RPM	9.52 RPM
SRP007412_liver	0.00 RPM	3.08 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3266 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3266 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4898
Gorilla gorilla	retro_ggor_3058
Pongo abelii	retro_pabe_3809
Macaca mulatta	retro_mmul_2635

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013,
Homo sapiens	ENSG00000162458	2 retrocopies	retro_hsap_4898, retro_hsap_778,
Gorilla gorilla	ENSGGOG00000015190	2 retrocopies	retro_ggor_3058, retro_ggor_645,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,
Pongo abelii	ENSPPYG00000001837	2 retrocopies	retro_pabe_3809, retro_pabe_751,
Pan troglodytes	ENSPTRG00000000208	2 retrocopies	retro_ptro_3266 , retro_ptro_544,
Pteropus vampyrus	ENSPVAG00000009000	1 retrocopy	retro_pvam_415,