RetrogeneDB ID: retro_mmul_949

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:53576512..53579215(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000023682
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NSMAF
• Ensembl ID: ENSMMUG00000017297
• Aliases: None
• Description: None

Sequence

>retro_mmul_949
TTTTCCTTGCTGCTGCTTAACTTGGAGGAGTACTACTCCGAACAGCATAGAGCCAATCACATTTTGCACAAGGGCAGTCA
CCATGAAAGAAAAATCAGAGGCTCCTTAAAAATATTGTTCAAAATCAGCGATTTTTGAACCAGATGCAATATCCCAGCCC
ATCATCAAGATTCCTTTGAGAGACTGTATAAAAACAGGAAAGCATAGAGAAAATGGAGCCAACAGACACTTCACAAAGGC
GAAATCTGGGAGTATTTCACTCATTTTCAGTCAGGTATATTTCATTAAAGAACATAATGTTGTCACACCATATAAAATAG
AAAGGGGCAAAATGGAGTATGTTTTTGAATTGGATGTTTCCGAGAAAGTGGAAGATGTTGTGGAGACGTTGCTTCAGCTT
CACAGAGCATCCTGCATTGACAAATTGGGTGACCAAACCGCCATGATAACAGCTATTTTGCAGTCTCGTTTGGCTAGAAC
ATCATTTGACAAAAACAGGTTCCAAAACATTTCTGAAAAGCTGCACATGGAATGCAAAGCAGAAATGGTGACGCCTCTGG
TGACTAATGCTGGACACGTGTGCATCACGGACACAAACCTCTATTTTCAGCCTCTCAATGGCTACCCGAAACCTGTGGTC
CAAATAACACTCCAAGATGTCCGCCACATCTACAAAAGGAGGCATGCCCTCATGCCTCTGGGCTTGGAAGTATTTTGCAC
AGAAGGTGATCTGTGTTCCGACATCTACCTAAAGTTCTATGAACCTCAAGATAGAGATGATCTCTATTTTTACATTGCCA
CATACCTAGAGCACCATGTGGCAGGGCACACTGCTGAGAGCTACATGCTGCAGTGGCAGCGTGGACTCCTTTCCAACTAT
CAGTACCTCCTTCACCTCAACAACCTGGCCGACCGCAGCTGCAACGACCTCTCCCAGTACCCTGTGTTTCCATGGATAAT
ACATGATTATTCCAGCTCAGAACTAGATTTGTCAAATCCAGGAAACTTCCGGGATCTTAGTAAGCCAGTGGGGGCCCTAA
ATAAGGAACGGCTGGAGAGGCTACTGACACGCTACCAGGAAATGCCTGAACCAAAGTTCATGCATGAGAGTCACTACTCT
TCCCCGGGTTATGTACTTTTTTTATCTTGTTAGGATTGCACCAGAGTATATGCTGTGCCTACAGAATGGAAGATTTGATA
ATGCAGATAGAATGTTCAACAGTATTGCAGAAACTTGGAAAAACAGTCTGGATGGTGCACCGGATTTTAAAGAGTTAATT
CCAGAATTCTATGGTGATGATGTAAGCTTTCTAGTCAATAGCCTGAAGTTGGATTTGGGAAAGAGACAAGGAGGACAGAT
GGCTGACGATGTGGAGCTTCCCCCTTGGGCCTCCAGTCCCGAGGACTTTCTCCAGAAGAGCAAAGATGCATTGGAAAGCA
ATTATGTGTCTGAACACCTTCTCGAGTGGATTGATCTAATATTTGGCTACAAACAAAAACGGAGTGGTGCAGTTGGGGCC
CATAATGTATTTCATCCCTTGACCTATGAAGGAGGTGTAGACTTGAACAGCATCCAGGATCCTGATGAGAAGGTAGCCAT
GCTTACGCAAATCTTGGAATTTGGGCAAACACCAAAACAACTATTTGTGACACCACACCCTCAAAGGATCACCCCAAAAT
TTAAAAGTTTGTCCCAGACCTCCAGTTATAACGCTTCTATGGCAGATTCCCCAGTCTCTCCAGGTGAAGAGTCTTTTGAA
GACCTGACCGAAGAAAGCAAAACACTGGCCTGGAATAACATCACCAAACTGCAGTTACATGAGCACTATAAAATCCACAA
AGAAGCAGTTACTGGAATCACAGTCTCTCGCAATGGATCTTCAGTCTTCACAACATCCCAAGATTCCACTTTGAAGATGT
TTTCTAAAGAATCGAAAATGCTACAAAGAAGCATATCATTTTCAAATATGGCTTTATCGTCTTGTTTACTTTTACCAGGA
GATGCCACTGTCATAACTTCTTCATGGGATAATAATGTCTATTTTTATTCCATAGCATTTGGAAGACGCCAGGACACATT
AATGGGACATGATGATGCTGTTGGTAAGATCTGTTGGCATGACAACAGGCTATATTCTGCATCGTGGGACTCTGCAGTGA
AGGTGTGGTCTGGTGTTCCTGCGGAGATGCCAGGCACCAAAAGACACCACTTTGACTTGCTAGCTGAGCTGGAACATGAT
GTCAGTGTAGAGACAATCAGTTTAAATCCTGCAAGCACACTGTTAGTTTCCGGCACCAAAGAAGGCACAGTGAATATTTG
GGACCTCAAAATGGCCACCTTAATGCACCAGATTCCATGCCATTCAGGGATTGTATGTGACACTGCTTTTAGCCCAGATA
GCCGCCACGTCCTCAGCACAGGAGCAGATGGCTGTCTTAATGTCATTGATGTACAGAGAGGAATGCTCATCTCCTCCATG
ACGTCAGATGAGCCCCAGAGGTGCCTTGTCTGGGATGGAAATTCCATTTTATCTGGAAGGCAGTCTGGTGAACTGCTTGT
TTGGAACCTCCTTGGAGCAAAAATCAGTGAGAGAACACAGGGCCACACATGTGCTGTGACATGTATATGGATGAATGAAC
AGTGTAGCAGTATCATATCACAGGAGGGGAAGACAGACAAATTATTTCTGGAAATTGCAGTAT

Alignment

ORF - retro_mmul_949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.57 %
• Parental protein coverage: 97.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FSLLLLNLEEYYFEQHRANHILHKGSHHERKIRGSLKI-CSKSAIFEPDAISQPIIKIPLRDCIKIGKHG
          FSLLLLNLEEYY.EQHRANHILHKGSHHERKIRGSLKI.CSKSAIFEPDAISQPIIKIPLRDCIK.GKH.
Retrocopy FSLLLLNLEEYYSEQHRANHILHKGSHHERKIRGSLKI>CSKSAIFEPDAISQPIIKIPLRDCIKTGKHR

Parental  ENGANRHFTKAKSGSISLIFSQVYFIKEHNVVAPYKIERGKMEYVFELDVPGKVEDVVETLLQLHRASCL
          ENGANRHFTKAKSGSISLIFSQVYFIKEHNVV.PYKIERGKMEYVFELDV..KVEDVVETLLQLHRASC.
Retrocopy ENGANRHFTKAKSGSISLIFSQVYFIKEHNVVTPYKIERGKMEYVFELDVSEKVEDVVETLLQLHRASCI

Parental  DKLGDQTAMITAILQSRLARTSFDKNRFQNISEKLHMECKAEMVTPLVTNPGHVCITDTNLYFQPLNGYP
          DKLGDQTAMITAILQSRLARTSFDKNRFQNISEKLHMECKAEMVTPLVTN.GHVCITDTNLYFQPLNGYP
Retrocopy DKLGDQTAMITAILQSRLARTSFDKNRFQNISEKLHMECKAEMVTPLVTNAGHVCITDTNLYFQPLNGYP

Parental  KPVVQITLQDVRRIYKRRHGLMPLGLEVFCTEDDLCSDIYLKFYEPQDRDDLYFYIATYLEHHVAEHTAE
          KPVVQITLQDVR.IYKRRH.LMPLGLEVFCTE.DLCSDIYLKFYEPQDRDDLYFYIATYLEHHVA.HTAE
Retrocopy KPVVQITLQDVRHIYKRRHALMPLGLEVFCTEGDLCSDIYLKFYEPQDRDDLYFYIATYLEHHVAGHTAE

Parental  SYMLQWQRGHLSNYQYLLHLNNLADRSCNDLSQYPVFPWIIHDYSSSELDLSNPGTFRDLSKPVGALNKE
          SYMLQWQRG.LSNYQYLLHLNNLADRSCNDLSQYPVFPWIIHDYSSSELDLSNPG.FRDLSKPVGALNKE
Retrocopy SYMLQWQRGLLSNYQYLLHLNNLADRSCNDLSQYPVFPWIIHDYSSSELDLSNPGNFRDLSKPVGALNKE

Parental  RLERLLTRYQEMPEPKFMYGSHYSSPGYVL-FYLVRIAPEYMLCLQNGRFDNADRMFNSIAETWKNCLDG
          RLERLLTRYQEMPEPKFM..SHYSSPGYVL.FYLVRIAPEYMLCLQNGRFDNADRMFNSIAETWKN.LDG
Retrocopy RLERLLTRYQEMPEPKFMHESHYSSPGYVL>FYLVRIAPEYMLCLQNGRFDNADRMFNSIAETWKNSLDG

Parental  ATDFKELIPEFYGDDVSFLVNSLKLDLGKRQGGQMVDDVELPPWASSPEDFLQKSKDALESNYVSEHLHE
          A.DFKELIPEFYGDDVSFLVNSLKLDLGKRQGGQM.DDVELPPWASSPEDFLQKSKDALESNYVSEHL.E
Retrocopy APDFKELIPEFYGDDVSFLVNSLKLDLGKRQGGQMADDVELPPWASSPEDFLQKSKDALESNYVSEHLLE

Parental  WIDLIFGYKQKGSGAVGAHNVFHPLTYEGGVDLNSIQDPDEKVAMLTQILEFGQTPKQLFVTPHPRRITP
          WIDLIFGYKQK.SGAVGAHNVFHPLTYEGGVDLNSIQDPDEKVAMLTQILEFGQTPKQLFVTPHP.RITP
Retrocopy WIDLIFGYKQKRSGAVGAHNVFHPLTYEGGVDLNSIQDPDEKVAMLTQILEFGQTPKQLFVTPHPQRITP

Parental  KFKSLSQTSSYNASMADSP---GEESFEDLTEESKTLAWNNITKLQLHEHYKIHKEAVTGITVSRNGSSV
          KFKSLSQTSSYNASMADSP...GEESFEDLTEESKTLAWNNITKLQLHEHYKIHKEAVTGITVSRNGSSV
Retrocopy KFKSLSQTSSYNASMADSPVSPGEESFEDLTEESKTLAWNNITKLQLHEHYKIHKEAVTGITVSRNGSSV

Parental  FTTSQDSTLKMFSKESKMLQRSISFSNMALSSCLLLPGDATVITSSWDNNVYFYSIAFGRRQDTLMGHDD
          FTTSQDSTLKMFSKESKMLQRSISFSNMALSSCLLLPGDATVITSSWDNNVYFYSIAFGRRQDTLMGHDD
Retrocopy FTTSQDSTLKMFSKESKMLQRSISFSNMALSSCLLLPGDATVITSSWDNNVYFYSIAFGRRQDTLMGHDD

Parental  AVSKICWHDNRLYSASWDSTVKVWSGVPAEMPGTKRHHFDLLAELEHDVSVDTISLNPASTLLVSGTKEG
          AV.KICWHDNRLYSASWDS.VKVWSGVPAEMPGTKRHHFDLLAELEHDVSV.TISLNPASTLLVSGTKEG
Retrocopy AVGKICWHDNRLYSASWDSAVKVWSGVPAEMPGTKRHHFDLLAELEHDVSVETISLNPASTLLVSGTKEG

Parental  TVNIWDLTTATLMHQIPCHSGIVCDTAFSPDSRHVLSTGADGCLNVIDVQTGMLISSMTSDEPQRCFVWD
          TVNIWDL..ATLMHQIPCHSGIVCDTAFSPDSRHVLSTGADGCLNVIDVQ.GMLISSMTSDEPQRC.VWD
Retrocopy TVNIWDLKMATLMHQIPCHSGIVCDTAFSPDSRHVLSTGADGCLNVIDVQRGMLISSMTSDEPQRCLVWD

Parental  GNSVLSGSQSGELLVWDLLGAKISERIQGHTGAVTCIWMNEQCSSIITGGEDRQIIF-WKLQY
          GNS.LSG.QSGELLVW.LLGAKISER.QGHT.AVTCIWMNEQCSSII.........F.WKLQY
Retrocopy GNSILSGRQSGELLVWNLLGAKISERTQGHTCAVTCIWMNEQCSSIISQEGKTDKLF>WKLQY

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	27.00 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	19.91 RPM
SRP007412_cerebellum	0.32 RPM	27.83 RPM
SRP007412_heart	0.06 RPM	18.08 RPM
SRP007412_kidney	0.23 RPM	16.43 RPM
SRP007412_liver	0.00 RPM	7.60 RPM
SRP007412_testis	0.08 RPM	7.73 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_949 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010583	3 retrocopies	retro_dnov_2269, retro_dnov_2290, retro_dnov_2361,
Macaca mulatta	ENSMMUG00000017297	1 retrocopy	retro_mmul_949 ,