RetrogeneDB ID: retro_mmul_1675

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:42854212..42856072(-)
• Located in intron of: ENSMMUG00000011232

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4761
• Ensembl ID: ENSMMUG00000018610
• Aliases: None
• Description: poly(A) polymerase alpha [Source:RefSeq peptide;Acc:NP_001252826]

Sequence

>retro_mmul_1675
CCGGTGACAACCCAGGGACCACCGCAGCAGGCGCCGCTGCCGAAGTGCTACGGCATCTCCTCGCCTATCAGCCTAGCGGT
CCCCAAGGAGACGGACTGCCTTCTCACCCAGAGGCTAATAGAAACCCTCAGGCCCTTCGGGGTCTTTGAAGAGGAAGAGG
AACTGCAGCGCAGGATTTTAGTTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGCGAAATCAGTGAAAGCAAG
AGCCTTCCCCAGTCTGTAATTGAAAACGTTGGCGGAAAGATTTTTACGTTTGGCTCTTACAGATTAGGAGTACATACGAA
AGGTGCAGATATTGACGCCTTGTGCGTTGCACCAAGGCATGTGGATCGAAGCGACTTTTTTACCTCATTCTATGTTAAAC
TGAAACTACAGGAGGAAGTAAAAGATTTAAGGGCTGTTGAGGAGGCATTTGTGCCAGTTATCAAACTGTGTTTTGATGGG
ATAGAGATTGATATTTTATTTGCAAGATTAGCACTACAGACTATTCCAGAAGATTTGGACCTAAGAGATGACAGTCTGCT
TAAAAATTTAGACATTAGATGCATAAGAAGCCTTAACGGTTGCCGGGTAACCGATGAAATTTTACATCTAGTGCCAAACA
TTGACAACTTCAGGTTGACTCTAAGAGCCATCAAACTGTGGGCCAAGTGCCACAATATCTATTCCAATATATTAGGTTTC
CTCGGAGGTGTTTCCTGGGCCATGCTGGTAGCAAGAACTTGTCAGCTTTATCCAAATGCAGTAGCGTCAACTCTCGTGCG
GAAATTCTTCTTGGTATTTTCGGAATGGGAATGGCCAAACCCAGTGTTACTGAAAGAGCCTGAAGAACGGAATCTTAACT
TGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCCATCATCACACCAGCATACCCACAGCAG
AACTCCACATACAACGTGTCTGTTTCAACCAGGATGGTCATGATTGAGGAGTTTAAACAGGGACTTGCTATCACACACGA
GATTTTGCTGAGTAAGGCTGAGTGGTCCAAACTCTTTGAAGCTCCAAGCTTCTTTCAGAAGTACAAGCATTATATTGTAC
TTCTGGCAAGTGCACCAACAGAAAAACAGCATTTAGAATGGGTGGGCTTGGTGGAATCAAAGATCCGAATCCTGGTTGGG
AGCTTGGAGAAGAATGAATTTATTACGCTGGCACATGTGAATCCACAGTCATTTCCAGCACCCAAAGAAAATCCTGATAT
GGAAGAATTTCGTACAATGTGGGTGATTGGTTTAGTGCTAAAAAAGCCAGAAAACTCTGAAATTCTCAGTATTGATCTCA
CCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAATGAATAGTAAGATGTTTGAGATGGGTATGAAAATT
ACTGCAATGCATTTAAGAAGAAAGGAGCTTCACCAGCTGCTGCCTCATCGTGTGCTTCAGGACAAGAAAGCACACGCAAC
AGAAGGTAGAAGATTGACAGATCTGAACGACAGCAGCTTTGACTTGTCTGCAGGCTGTGAAAACAGCATGTCTGTGCCTT
CATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAGGGTAGAAATAGTCCTGCCCTGGCTGTAATGACA
GCATCGATGGCTAACGTACAGGCTACTGAAATTTCCTTGCAACAGATGAATACCAGTGAAAGTTCAGGGGTTGCATTAAA
TGAAAGTATTCCTCACGCTGTCTCTCAGCCTGCCATTTCTCCATCACCAAAGGCCATGGTCGCCAGAGTTGTTTCTTCGA
CATGTCTCATAAGCCATCCA

Alignment

ORF - retro_mmul_1675 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 83.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVTTQGSQQTQPPQKHYGITSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVK
          PVTTQG..Q..P..K.YGI.SPISLA.PKETDC.LTQ.LIETL.PFGVFEEEEELQRRIL.L.KLNNLVK
Retrocopy PVTTQGPPQQAPLPKCYGISSPISLAVPKETDCLLTQRLIETLRPFGVFEEEEELQRRILVLEKLNNLVK

Parental  EWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEV
          EWIREISESK.LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFY.KLKLQEEV
Retrocopy EWIREISESKSLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYVKLKLQEEV

Parental  KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
          KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
Retrocopy KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL

Parental  VPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPN
          VPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPN
Retrocopy VPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWPN

Parental  PVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILL
          PVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILL
Retrocopy PVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILL

Parental  SKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
          SKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
Retrocopy SKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA

Parental  PKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL
          PKENPD.EEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKI.AMH..RK.L
Retrocopy PKENPDMEEFRTMWVIGLVLKKPENSEILSIDLTYDIQSFTDTVYRQAMNSKMFEMGMKITAMHLRRKEL

Parental  HQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGRNSPAPAV
          HQLLP..VLQ.KK.H.TEG..LT.LNDSS.DLS....NSMSVPS.TS..KT.PL.S..SSQGRNSPA.AV
Retrocopy HQLLPHRVLQDKKAHATEGRRLTDLNDSSFDLSAGCENSMSVPSSTSTMKTGPLIS--SSQGRNSPALAV

Parental  TAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPP
          ..AS..N.QATE.S..Q.N.SESSG....ESIP....QPAISP.PK..V.RVVSST.L...P
Retrocopy MTASMANVQATEISLQQMNTSESSGVALNESIPHAVSQPAISPSPKAMVARVVSSTCLISHP

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	61.07 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	50.77 RPM
SRP007412_cerebellum	1.36 RPM	66.06 RPM
SRP007412_heart	0.18 RPM	43.22 RPM
SRP007412_kidney	0.23 RPM	74.65 RPM
SRP007412_liver	0.00 RPM	21.93 RPM
SRP007412_testis	159.71 RPM	215.91 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1675 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1675 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_30
Pan troglodytes	retro_ptro_2595
Gorilla gorilla	retro_ggor_202
Pongo abelii	retro_pabe_3113
Callithrix jacchus	retro_cjac_1763
Mus musculus	retro_mmus_37
Rattus norvegicus	retro_rnor_863
Bos taurus	retro_btau_1078
Canis familiaris	retro_cfam_1783

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675 ,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,