RetrogeneDB ID: retro_ptro_544

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:46251289..46251958(+)
• 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_544
GGATGTCCACCCCCTCCTCCTGTCCTGGATGGTTAGGACGTGCTTCCCCACCTGGACCTCCTCCCACCTGCTTCACCGCC
CCCGCCGGTGCTCTTGCCTTCTGAAGACGAGACTCCTGCTCTAATGGGGGCCTCACTTATTGCGGACTTAGAGCAGCTGC
ACCTGCCCCCGTCCCCACCCCCACCACAGGCCCCTGCGGAGAGACCTTCAGTCCAGCCTGGGCCGGATCCCCTCAGGCCC
GTGGAAAAAGAGCTGCCGCCTCCCCCAGCAGAGCCTGTTGAGAGAGAGGCGTCCACAGACATCCGTGCCTTCTGCCATAA
GACTGTGTCCCCCCAGGAGCTGGCTGTGGAGGCCATGAAGAGGCACTACCATGTCCAGTTCTTCACATGCCGTATCTGCC
GCCGCCAGCTGGCTGGGCAGAGCTTCTATCAGAAGAATATGCGACCCCTCTGCGAACCCTGCTGCCAGGACACGCTGCAG
AAGTGCAGCAAGTGTGGCGAGGTGGTCTGGGAGCACATCATCAGGGCCCCGGGCCAGGCCTTCCACCCCACCTGCTTCAC
GTGTGTGACCTGCGCCCGGTGCATCGGGGATGAGAGCTTTGCCCCGGGCAGCCAGAAGGAGGTGTACTGCCTGGACGACT
TCTACAGGAAATTTGCCCCCGTCTGCAGC

Alignment

ORF - retro_ptro_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.06 %
• Parental protein coverage: 59.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCPPPPPVLDGEDVLPDLDLLPPPPPPPPVLLPSEEEAPAPMGASLIADLEQLHLSPPPPPPQAPAEGPS
          GCPPPPPVLDG.DVLP.LDLLPP..PPPPVLLPSE.E.PA.MGASLIADLEQLHL.P.PPPPQAPAE.PS
Retrocopy GCPPPPPVLDG*DVLPHLDLLPPASPPPPVLLPSEDETPALMGASLIADLEQLHLPPSPPPPQAPAERPS

Parental  VQ--PCPLRPVEEELPPPPAEPVEKGASTDICAFCHKTVSPRELAVEAMKRQYHAQCFTCRTCRRQLAGQ
          VQ..P.PLRPVE.ELPPPPAEPVE..ASTDI.AFCHKTVSP.ELAVEAMKR.YH.Q.FTCR.CRRQLAGQ
Retrocopy VQPGPDPLRPVEKELPPPPAEPVEREASTDIRAFCHKTVSPQELAVEAMKRHYHVQFFTCRICRRQLAGQ

Parental  SFYQKDGRPLCEPCYQDTLERCGKCGEVVRDHIIRALGQAFHPSCFTCVTCARCIGDESFALGSQNEVYC
          SFYQK..RPLCEPC.QDTL..C.KCGEVV..HIIRA.GQAFHP.CFTCVTCARCIGDESFA.GSQ.EVYC
Retrocopy SFYQKNMRPLCEPCCQDTLQKCSKCGEVVWEHIIRAPGQAFHPTCFTCVTCARCIGDESFAPGSQKEVYC

Parental  LDDFYRYEKGLCT
          LDDFYR.....C.
Retrocopy LDDFYRKFAPVCS

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	0.04 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_544 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_544 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_778
Pongo abelii	retro_pabe_751
Macaca mulatta	retro_mmul_1095

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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,