RetrogeneDB ID: retro_mmul_689

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214725764:3767..4676(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009538
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.1586
• Ensembl ID: ENSMMUG00000007904
• Aliases: None
• Description: general transcription factor IIF subunit 1 [Source:RefSeq peptide;Acc:NP_001247759]

Sequence

>retro_mmul_689
ATGGCGGCCCTAGCCCTAGCAGCCAGAACGTCACTAAATACGTCGGTCGAGTTCCCAAGAATACAACCAAAAAATGTAAC
ATCATGGCTTTTAATGCAGCCAATACAGTCAGCTTTGCTACGTGGAATCAGGCTCGGCTGAAGCGGGACTTGAGCAACAA
GAAAATCTACCAGGAGGAGGAGATGTCTGAATCCGCGCGGGCAGCGAGTTCAACCGCAAGCTTCGGGAGGAGGCTCGGAG
GAAGAAGTACCGCATCGTCCTCAAGGAGTTCTGGCCCGGGGACCGGCCCTGGCTGCTCCCGGTCAACGGCAAATCGGGCA
GGAAGTTCGAGAGCATCAAGAAGGGAGGGTGACAGAGAACACGTCTTACTACATCTTCACCCAGTGCCCTGACGGGGTCT
TGGAGGCCTTCCCCGTGCACAACTGGTACAATTTCACGCTGCCGGCCCGGTAGGCACCGCACGCTCACTGCCGAGGAGCC
GGAGGAGGAGTGGGAGAGGAGGAACAAGGTGCTGAACCACTTCAGCATCATACAGCAGCGGCGGCTCAAGGATCAGGACC
AGGAGGAGGACAAGGAGGAGAAGGAGAAACGCGGTCGCAGGAAGGCAAACGAGCTGCGCATCCACGACCTGGAGATGTCA
TCCGATGCCAGCCACGCCAGCGGTGAGGAGAAGGCAGAGCCCCCAAGGCCAAGAACAAGGAGCCGCTGGCCGAGGGCGGC
AGGAAAAAGAAGAAGAAGGGCTCAGACGATGAGGCCTTCGAGGACAGCTGTGATGGGGACCTCGAGGGCCAGGAGGTGAA
CTACATGTCGGACGGCTCCAGCAGCTCCCAGGATGAGCCTGGGAGCAAGGCCAAGGAGCCCCAGCAGGAGGAGGGGCCCA
AGGGTGTTGATGAGCAGAGCAACAGTAGT

Alignment

ORF - retro_mmul_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.17 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAALG-PSSQNVTEYVVRVPKNTTKKYNIMAFNAADKVNFATWNQARLERDLSNKKIYQEEEMPESG-AG
          MAAL..PSSQNVT.YV.RVPKNTTKK.NIMAFNAA..V.FATWNQARL.RDLSNKKIYQEEEM.ES..AG
Retrocopy MAALA<PSSQNVTKYVGRVPKNTTKKCNIMAFNAANTVSFATWNQARLKRDLSNKKIYQEEEMSESA<AG

Parental  SEFNRKLREEARRKKYGIVLKEFRPEDQPWLLRVNGKSGRKFKGIKKGG-VTENTSYYIFTQCPDGAFEA
          SEFNRKLREEARRKKY.IVLKEF.P.D.PWLL.VNGKSGRKF..IKKGG.VTENTSYYIFTQCPDG..EA
Retrocopy SEFNRKLREEARRKKYRIVLKEFWPGDRPWLLPVNGKSGRKFESIKKGG<VTENTSYYIFTQCPDGVLEA

Parental  FPVHNWYNFTPLAR-HRTLTAEEAEEE-WERRNKVLNHFSIMQQRRLKDQDQDEDEEEKEKRGRRKASEL
          FPVHNWYNFT..AR........E..EE.WERRNKVLNHFSI.QQRRLKDQDQ.ED.EEKEKRGRRKA.EL
Retrocopy FPVHNWYNFTLPAR>RHRTLTAEEPEEEWERRNKVLNHFSIIQQRRLKDQDQEEDKEEKEKRGRRKANEL

Parental  RIHDLEDDLEMSSDASDASGEE-GGRAPKAKKKVPLAKGGRKKKKKKGSDDEAFEDSDDGDFEGQEVDYM
          RIHDLE....MSSDAS.ASGEE..GRAPKAK.K.PLA.GGR.KKKKKGSDDEAFEDS.DGD.EGQEV.YM
Retrocopy RIHDLE----MSSDASHASGEE<EGRAPKAKNKEPLAEGGR-KKKKKGSDDEAFEDSCDGDLEGQEVNYM

Parental  SDGSSSSQDEPESKAKPPQQEEGPKGVDEQSDSS
          SDGSSSSQDEP.SKAK.PQQEEGPKGVDEQS.SS
Retrocopy SDGSSSSQDEPGSKAKEPQQEEGPKGVDEQSNSS

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	33.39 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	98.61 RPM
SRP007412_cerebellum	0.06 RPM	33.32 RPM
SRP007412_heart	0.00 RPM	32.33 RPM
SRP007412_kidney	0.00 RPM	26.06 RPM
SRP007412_liver	0.00 RPM	12.51 RPM
SRP007412_testis	0.38 RPM	80.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_689 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000007904	1 retrocopy	retro_mmul_689 ,
Sarcophilus harrisii	ENSSHAG00000010846	1 retrocopy	retro_shar_55,