RetrogeneDB ID: retro_mmul_947

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:41630888..41632203(-)
• Located in intron of: ENSMMUG00000002011

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12220
• Ensembl ID: ENSMMUG00000008827
• Aliases: None
• Description: apoptosis inhibitor 5 [Source:RefSeq peptide;Acc:NP_001244862]

Sequence

>retro_mmul_947
CAGTTAGACTTCTGTGAGGATGAAGATGTATCTATTCGATGTCAAGCAATTAAAGAACTGCCTCAATTTGCCACTGGAGA
AAATCTTCCTTGAGTGGCAGATATACTAATGCAACTTTTGGAGACAGATGACTCTGCAGAATTTAACCTAGTGAACAATG
CCCTGTTAAGTATATTTAAGATGGATGGAAAAGGGACTTTAGTTTCGTTGTTCAGCCAAATACTTCAAGGAGAGGACATT
GTTAGAGAATGAGCAATTAAGTTCCTTTCTACAAAACTTAAGACTTTACCAGATGAATTCATAACAAAGGAAGTGGAAGA
GCTTCTACTAACTGAATCCAAACCAGTCCTAGACGATGTGACTGATGAAGAATTTGCTCTATTCATGAAATACTGCCTGG
GTTAAAAAGCTTACAGACAGTAAGTGGAAGACAGCAACTTGTAGAATTGGTGGCACAGGCCGACCTAGAACAGACCTCCA
ATCCCTCTGATCCTGACTGTGTGGACAGGCTCTCACAGTGCACTCGGCAGGCAGTACCCTTCTCTAAAACTGTCCATTCC
ATAAGGTTTGTGACATATTTCTGTGAGCAGGTTCTCCCTAGCCTTGGTATCTTAACTATCCCAGTGGAAGGTCTTGATAT
ACAGTTGGAGGTATTGAAATTGTTGGTGGAGATGAGTTCATTTTGTGGTGACATGGAAAAACTGGAAACAAATTTAAGGA
AACGATTTGATAAGTTATTGGAATACATGCCCCTCCCTTCAGAAGAACCAGAAAATGGAGAGAATGCTGGTGATGAAGAG
CCCAAGCTACGGTTCAGTTATGTGGAATGTTTGTTGTACAGTTTTCACCAGTTGGGCCGAAAACTTCAGATTTCTTAACA
GCCAAACTGAATGCAGAAAAACCCAAAGATTTCAAAATCAGGCTGCAATACTTTGCACAAGGCCTGCAAGTTTATATTAG
ACAACTTCGCTTAGCTCTCCAGGGTAAAACGGGTGAGAACAGAAGAGAACAGAAAACAGAAGAGAACTAGATTAAAGTTG
TTGCATTGAAAGCAACAAACAATATCAATGTTTTGATCAAGGATCTCTTCCACATTCCTCCTTCTTGTAAGAGCACAGTA
ACACTGTCCTGGAAACCTGTATGAAAGGTTGAGATTGGGCAAAAGAGAGCCAGTGGATATGCAACTTCAGGTTCACCACC
CAAGAAATCTTCAGCAGTACAAAAAAGAGATGCCAGGCAGATTTATAATCCTCCCAGTGAGAAATTTAGCAGCAATTTGG
GCAACTTTAATTATGAGAGGAGCCTTCAGGGAAAG

Alignment

ORF - retro_mmul_947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.04 %
• Parental protein coverage: 86.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLDLCEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGL
          QLD.CEDEDVSIR.QAIKELPQFATGENLP.VADIL.QLL.TDDSAEFNLVNNALLSIFKMD.KGTL..L
Retrocopy QLDFCEDEDVSIRCQAIKELPQFATGENLP*VADILMQLLETDDSAEFNLVNNALLSIFKMDGKGTLVSL

Parental  FSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFMK-ILSGLKSLQ
          FSQILQGEDIVRE.AIKFLSTKLKTLPDE..TKEVEEL.LTESK.VL.DVT.EEF.LFMK.IL.GLKSLQ
Retrocopy FSQILQGEDIVRE*AIKFLSTKLKTLPDEFITKEVEELLLTESKPVLDDVTDEEFALFMK<ILPGLKSLQ

Parental  TVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTT
          TVSGRQQLVELVA.QADLEQT.NPSDPDCVDRL.QCTRQAVP.FSK.VHS.RFVTYFCEQVLP.LG.LT.
Retrocopy TVSGRQQLVELVA-QADLEQTSNPSDPDCVDRLSQCTRQAVP-FSKTVHSIRFVTYFCEQVLPSLGILTI

Parental  PVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVEC
          PVEGLDIQLEVLKLL.EMSSFCGDMEKLETNLRK.FDKLLEYMPLP.EE.ENGENAG.EEPKL.FSYVEC
Retrocopy PVEGLDIQLEVLKLLVEMSSFCGDMEKLETNLRKRFDKLLEYMPLPSEEPENGENAGDEEPKLRFSYVEC

Parental  LLYSFHQLGRKL-PDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGE---ALKTEENKIK
          LLYSFHQLGRKL..DFLTAKLNAEK.KDFKIRLQYFA.GLQVYIRQLRLALQGKTGE.....KTEEN.IK
Retrocopy LLYSFHQLGRKL<SDFLTAKLNAEKPKDFKIRLQYFAQGLQVYIRQLRLALQGKTGENRREQKTEEN*IK

Parental  VVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIY
          VVALK.TNNINVLIKDLFHIPPS.KSTVTLSWKPV.KVEIGQKRAS...TSGSPPKKSSA..KRDARQIY
Retrocopy VVALKATNNINVLIKDLFHIPPSCKSTVTLSWKPV*KVEIGQKRASGYATSGSPPKKSSAVQKRDARQIY

Parental  NPPSGKYSSNLGNFNYERSLQGK
          NPPS.K.SSNLGNFNYERSLQGK
Retrocopy NPPSEKFSSNLGNFNYERSLQGK

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	0.11 RPM	74.63 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	49.82 RPM
SRP007412_cerebellum	0.06 RPM	81.88 RPM
SRP007412_heart	0.00 RPM	30.33 RPM
SRP007412_kidney	0.00 RPM	46.83 RPM
SRP007412_liver	0.00 RPM	24.50 RPM
SRP007412_testis	0.04 RPM	41.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_947 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_947 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2350
Pan troglodytes	retro_ptro_1720
Gorilla gorilla	retro_ggor_1784

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011993	1 retrocopy	retro_cpor_861,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Macaca mulatta	ENSMMUG00000008827	1 retrocopy	retro_mmul_947 ,
Mus musculus	ENSMUSG00000027193	1 retrocopy	retro_mmus_2908,
Pongo abelii	ENSPPYG00000003345	1 retrocopy	retro_pabe_3805,
Vicugna pacos	ENSVPAG00000012428	1 retrocopy	retro_vpac_289,