RetrogeneDB ID: retro_mmul_1519

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:79070133..79071194(-)
• Located in intron of: ENSMMUG00000031881

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISG20L2
• Ensembl ID: ENSMMUG00000000037
• Aliases: None
• Description: interferon-stimulated 20 kDa exonuclease-like 2 [Source:RefSeq peptide;Acc:NP_001244602]

Sequence

>retro_mmul_1519
ATGTCTACTTTACTGCTCAATCTGGATTTTGGGGAACCTCCTCCCAAAAAGGCATTAGAAGGAAATGCCAAGCACTGAAA
TTTTGTCAAGAAGCGGAGGCTCTTAGAACGGAGAGGCTTTCTGAGTAAAAAGAACCAACCCCCTAGCAAGGCGCCTAAGT
TGCACTCTGAACCTCCAAAGAAAGGGGAAGCTCCTACAGTGGATGGCACTTGAAGACCCCTTCCTTCCCAAAAAGAAGAA
GACAGCTGCCTCTAGCAATGGGTCAGGACAGCCCCTGGACAAGAAAGCTGCAGTGTCTTGGCTGATCCCTGCCCCTTCAA
AAAAGGCTGATTCTGTTGCTGCTAAAGTAGATTTGCTGGGGGAGTTCCAGAGTGCCCTTCCAAAGATCAATAGTCACCCA
ACCTGCTCTCAGAAGAAGGGCTCCCAGAAGAAATCCTCTAAGAAGAACCATCCTCAGAAGAATGCCCCACAGAACTCCAC
CCAAGCTCATTCAGAGAATAAATGCTCCGGAATATCCCAGAAGTTGCCACAGAAGATGGTGGCAATTGACTGTGAGATGG
TGGGCACAGGATCAAAGGGGCATGTTAGTTCCTTGGCTCAATGTAGCATTGTCAACTACAATGGAGATGTGCTTTATGAC
GAGTACATTCTTTCCCCCTGCCACATTGTGGACTACCGAACCAGATGGAGTGGTATCCGGAAGCACCACGTGGTGAATGC
CACACCCTTCAAGATTGCTCGAGGCCAGATCTTGAAGATACTCACAGGGAAGACAGTGGTGGGACATGCCATCCACAATG
ACTTCAAAGCCCTTCAGTACTTTCACCCCAAGTCCCTCACCTGTGACACCTCCCATAGCACCCCCCTCAACCTGGAAGGC
TCACTGCCCGGAGAATGCCACCATGTCTCTGAAGCATCTCACCAAGAAGCTGCTAAACTGGGATATCCAGGTTGGGAAGA
GTGGACATTCCTCTGTGGAAGATGCCCAGGCCACCGTGGAGCTGTACAAGTTGGTTGAAGTCGAGTGGGAAGAGCACCTA
GCCCAGAATCCCCCTAAAGAC

Alignment

ORF - retro_mmul_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTLLLNLDFGEPPPKKALEGNAKHRNFVKKRRLLERRGFLSKKNQPPSKAPKLHSEPPKKGETPMVDGT
          MSTLLLNLDFGEPPPKKALEGNAKH.NFVKKRRLLERRGFLSKKNQPPSKAPKLHSEPPKKGE.P.VDGT
Retrocopy MSTLLLNLDFGEPPPKKALEGNAKH*NFVKKRRLLERRGFLSKKNQPPSKAPKLHSEPPKKGEAPTVDGT

Parental  -WKTPSFPK-KKKTAACSNGSGQPLDKKAAVSWLTPAPSKKADSVAAKVDLLGEFQSALPKINSHPTRSQ
          ..KTPSFPK.KKKTAA.SNGSGQPLDKKAAVSWL.PAPSKKADSVAAKVDLLGEFQSALPKINSHPT.SQ
Retrocopy <LKTPSFPK<KKKTAASSNGSGQPLDKKAAVSWLIPAPSKKADSVAAKVDLLGEFQSALPKINSHPTCSQ

Parental  KKGSQKKSSKKNHPQKNAPQNSTQAHSENKCSRISQKLPQKMVAIDCEMVGTGPKGHVSSLARCSIVNYN
          KKGSQKKSSKKNHPQKNAPQNSTQAHSENKCS.ISQKLPQKMVAIDCEMVGTG.KGHVSSLA.CSIVNYN
Retrocopy KKGSQKKSSKKNHPQKNAPQNSTQAHSENKCSGISQKLPQKMVAIDCEMVGTGSKGHVSSLAQCSIVNYN

Parental  GDVLYDEYILPPCHIVDYRTRWSGIRKQHMVNATPFKIARGQILKILTGKIVVGHAIHNDFKALQYFHPK
          GDVLYDEYIL.PCHIVDYRTRWSGIRK.H.VNATPFKIARGQILKILTGK.VVGHAIHNDFKALQYFHPK
Retrocopy GDVLYDEYILSPCHIVDYRTRWSGIRKHHVVNATPFKIARGQILKILTGKTVVGHAIHNDFKALQYFHPK

Parental  SLTRDTSHIPPLNR-KADCPENATMSLKHLTKKLLNRDIQVGKSGHSSVEDAQATMELYKLVEVEWEEHL
          SLT.DTSH..PLN..KA.CPENATMSLKHLTKKLLN.DIQVGKSGHSSVEDAQAT.ELYKLVEVEWEEHL
Retrocopy SLTCDTSHSTPLNL>KAHCPENATMSLKHLTKKLLNWDIQVGKSGHSSVEDAQATVELYKLVEVEWEEHL

Parental  AQNPPKD
          AQNPPKD
Retrocopy AQNPPKD

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	15.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.63 RPM
SRP007412_cerebellum	0.00 RPM	19.63 RPM
SRP007412_heart	0.06 RPM	8.07 RPM
SRP007412_kidney	0.12 RPM	12.79 RPM
SRP007412_liver	0.04 RPM	11.52 RPM
SRP007412_testis	0.87 RPM	382.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1519 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006559	1 retrocopy	retro_fcat_1999,
Macaca mulatta	ENSMMUG00000000037	1 retrocopy	retro_mmul_1519 ,
Nomascus leucogenys	ENSNLEG00000012742	1 retrocopy	retro_nleu_3048,
Rattus norvegicus	ENSRNOG00000011402	2 retrocopies	retro_rnor_2836, retro_rnor_463,