RetrogeneDB ID: retro_mmul_1095

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:25988672..25989546(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSMMUG00000032243
• Aliases: None
• Description: None

Sequence

>retro_mmul_1095
TGTCCACCCCCTCCTCCTGTCCTGGATGGTTAGGACGTGCTTCCTCACCTGGACCTCCTCCCACCCGCTTCACGGTCCCC
TCCGGGGCACGTGCCTTCTGAAGAGGAGGCTCCTGCTCCAATGGGGGCCTCACTTATTGCGGACTTAGAGCAGCTGCGCC
TGCCCCCGTCCCCACCCCCACCACAGACCCCAGCGGAGGGACCATCGGTCCAGCCTGGGCCGGATACCCTCAGACCCTTG
GAAAAAGAGCTGCCGCCTCCCCCAGCAGAGCTTGTTGAGAGAGAGGCGTCCACAGACATCCGTGCCTTCTACCATAAGAC
TGTGTCCCCCGCAAGAACTGGCTGTAGATGCCATGAAGAGGCAGTACCATGCCCAGTACTCCACGTGCCGTACCAGCCGC
CGCCAGCTGGCCGGGCAGAGCTTCTACCAGAAGGATGCGCGACCCCTCTGCGAACCCTGCTGCCAGGACACGCTGCAGAA
GTTCAGCAAGTGTGGCGAGGTGGTCCGGGAGCACATCATCAGGGCCCTGGGCCAGGCCTTCCACCCCTCCTGCTTCACGT
GTGTGACCCGCGCCTGGTGCATCGGGGATAAAAGCTTTGCCCCGGGCAGCCAGAACGAGGTGTACTCCCTGGACAACTTC
TACAGGAAATTTGCCCCCATCTGCAGCATCTGTGAGAATCTCATAATTCCTCGGGATGGGAAGTATGTCTTCAAAATCGA
GTGCACTGGAGGCAATTTCCATGAAAATTGCTACAGGTATAAGGACTGCAGGATCCTCCTGTCTATCGAGCCCACGGACC
AAGGCTGCTACCCCCTCAACAATCGTCTCTTCTGCAAGGCGTGCCACCTGAAGCAGAGTGCTGCGGGGTGCTGC

Alignment

ORF - retro_mmul_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 77.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CPPPPPVLDGEDVLPDLDLLPPPPPPPPVLLPSEEEAPAPMGTSLIADLQQLHLSPPPPPPPPQAPAEGP
          CPPPPPVLDG.DVLP.LDLLPP....PP...PSEEEAPAPMG.SLIADL.QL.L..PP.PPPPQ.PAEGP
Retrocopy CPPPPPVLDG*DVLPHLDLLPPASRSPPGHVPSEEEAPAPMGASLIADLEQLRL--PPSPPPPQTPAEGP

Parental  SVQPGP--LRPVEEELPPPPAEPVEKEASTDICAFCHKTVSP-RELAVEAMKRQYHAQCFTCRTCRRQLA
          SVQPGP..LRP.E.ELPPPPAE.VE.EASTDI.AF.HKTVSP..ELAV.AMKRQYHAQ..TCRT.RRQLA
Retrocopy SVQPGPDTLRPLEKELPPPPAELVEREASTDIRAFYHKTVSP>QELAVDAMKRQYHAQYSTCRTSRRQLA

Parental  GQSFYQKDGRPLCEPCYQDTLEKCGKCGEVVQDHIIRALGQAFHPSCFTCVTCARCIGDESFALGSQNEV
          GQSFYQKD.RPLCEPC.QDTL.K..KCGEVV..HIIRALGQAFHPSCFTCVT.A.CIGD.SFA.GSQNEV
Retrocopy GQSFYQKDARPLCEPCCQDTLQKFSKCGEVVREHIIRALGQAFHPSCFTCVTRAWCIGDKSFAPGSQNEV

Parental  YCLDDFYRKFAPVCSICENPIIPRDGKDAFKIECMGRNFHENCYRCEDCRILLSVEPTDQGCYPLNNRLF
          Y.LD.FYRKFAP.CSICEN.IIPRDGK..FKIEC.G.NFHENCYR..DCRILLS.EPTDQGCYPLNNRLF
Retrocopy YSLDNFYRKFAPICSICENLIIPRDGKYVFKIECTGGNFHENCYRYKDCRILLSIEPTDQGCYPLNNRLF

Parental  CKPCHVKRSAAGCC
          CK.CH.K.SAAGCC
Retrocopy CKACHLKQSAAGCC

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	0.00 RPM	1.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.30 RPM
SRP007412_cerebellum	0.00 RPM	1.36 RPM
SRP007412_heart	0.00 RPM	22.73 RPM
SRP007412_kidney	0.00 RPM	7.86 RPM
SRP007412_liver	0.00 RPM	1.90 RPM
SRP007412_testis	0.00 RPM	1.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1095 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1095 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_778
Pan troglodytes	retro_ptro_544
Pongo abelii	retro_pabe_751

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 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	ENSMMUG00000021252	1 retrocopy	retro_mmul_2377,
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,