RetrogeneDB ID: retro_mmul_1904

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:120487824..120488467(+)
• Located in intron of: ENSMMUG00000021347

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOSL1
• Ensembl ID: ENSMMUG00000008653
• Aliases: None
• Description: None

Sequence

>retro_mmul_1904
GGTACAGCCTCATTTCCTGGGGCCCAGCAGTTACCCCAGGCCTCTGAACTACCCCCACAACCCCAGCCAGGAGTCATCCG
GGCCCCAGGGCCGCCTCCAGGGGTACGTCCAAGGCCTTGTGAACAGATCAACCTGGAGGAAGAGGAGCGCGCCGAGTAAG
GCGGGAGCGGAACAAGCTGGCTGCGGCCAAGTGCAGGAACCGGAGGAAGGAACTGACCGACTTCCTGCAGGTGGAGACTG
ACAAACTGGAAGATGAGAAATCCGCGCTCCCGAGAGAGATTGAGGAGCTGCAGAAGCAGAAGGAGCGCCTGGAGCTGGTG
CTGGAAGCCCACTGACTCATCTGCAAAATCCCCGAAGGAGCCAAGGAGGGGGACACAGGCGGTACCAGCAGCACCAGCAG
CCCGTCAGCCCCCTGCCGCCCTGTACCTTGTATCTCCCTTTCCCCAGGGCCTGTACTTGAACCTGAGGCACTGCACACCC
GCACGCTTATGACCACACCCTCCCTAACTCCTTTCACCCCCAACCTGGTCTTCACCTATGCCAGCACTCCTGAGCCCTGT
GCCTCAGCTCGTGGCAAAGGAGTAGCAGCAGCAGCGGAGACCCACCCTCTGACCCCCTTGGCTCTCCACCTGTTCTCGCT
TTG

Alignment

ORF - retro_mmul_1904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.03 %
• Parental protein coverage: 78.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPSSYPRPLTYPQYS--PPQPRPGVIRALGPPPGVRRRPCEQISPEEEER-RRVRRERNKLAAAKCRNRR
          G..S.P.....PQ.S..PPQP.PGVIRA.GPPPGVR.RPCEQI..EEEER.RRVRRERNKLAAAKCRNRR
Retrocopy GTASFPGAQQLPQASELPPQPQPGVIRAPGPPPGVRPRPCEQINLEEEER<RRVRRERNKLAAAKCRNRR

Parental  KELTDFLQAETDKLEDEKSGLQREIEELHKQKERLELVLEAHRPICKIPEGAKEGDTGSTSGMSSPPAPC
          KELTDFLQ.ETDKLEDEKS.L.REIEEL.KQKERLELVLEAH..ICKIPEGAKEGDTG.TS..SSP.APC
Retrocopy KELTDFLQVETDKLEDEKSALPREIEELQKQKERLELVLEAH*LICKIPEGAKEGDTGGTSSTSSPSAPC

Parental  RPVPCISLSPGPVLEPDALHTPTLMTTPSLTPFTPSLVFTYPSTPEPCASAHRKS-SS-SSGDPSSDPLG
          RPVPCISLSPGPVLEP.ALHT.TLMTTPSLTPFTP.LVFTY.STPEPCASA..K..SS.SSGDP.SDPLG
Retrocopy RPVPCISLSPGPVLEPEALHTRTLMTTPSLTPFTPNLVFTYASTPEPCASARGKG<SSSSSGDPPSDPLG

Parental  SPTLLAL
          SP..LAL
Retrocopy SPPVLAL

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	0.22 RPM	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.24 RPM
SRP007412_cerebellum	0.13 RPM	0.26 RPM
SRP007412_heart	0.12 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.04 RPM	0.08 RPM
SRP007412_testis	0.45 RPM	8.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1904 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1904 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2981
Pan troglodytes	retro_ptro_2016
Pongo abelii	retro_pabe_2471

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175592	1 retrocopy	retro_hsap_2981,
Macaca mulatta	ENSMMUG00000008653	1 retrocopy	retro_mmul_1904 ,
Nomascus leucogenys	ENSNLEG00000005945	1 retrocopy	retro_nleu_1509,
Pongo abelii	ENSPPYG00000003041	1 retrocopy	retro_pabe_2471,
Pan troglodytes	ENSPTRG00000003901	1 retrocopy	retro_ptro_2016,