RetrogeneDB ID: retro_mmus_37

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:142527957..142529886(-)
• Located in intron of: ENSMUSG00000029576

Retrocopy information

• Ensembl ID: ENSMUSG00000074817
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Papola
• Ensembl ID: ENSMUSG00000021111
• Aliases: Papola, Pap, PapIII, Plap
• Description: poly (A) polymerase alpha [Source:MGI Symbol;Acc:MGI:109301]

Sequence

>retro_mmus_37
ATGATGCCATTTGCGGTGACCACCCAAGGAGCACAACAACCGGCTCCCGCCCCGAAGCAGTTCGGCATATCGTCCCCCAT
CAGCCTGGCCGCCCCCAAGGACACAGACCGCGAACTCACCCAGAAGCTGATCGAGACCCTCCAGCCCTTCGGGGTGTTTG
AAGAGGAAGAGGAACTGCAGCGCAGGATTTTAATTTTGCAGAAATTAAATAATCTGGTGAAGGAATGGATCCGAGAAATC
AGTGAAAGCAGGAATCTTCCACAAGCTGTAATTGAGAATGTTGGGGGGAAAATTTTTACGTTCGGCTCTTACCGATTAGG
AGTACACACGAAAGGTGCAGATATCGATGCTTTGTGCGTTGCACCAAGACACGTGGATCGAAATGACTTTTTCACCTCCT
TCTATGACAAATTGAAACTACAAGAGGAAGTAAAAGATTTAAGAGCTGTTGAGGAGGCCTTTGTGCCGGTTATCAAACTG
TGTTTTGATGGAATAGAGATTGATATTTTGTTTGCAAGATTAGCATTGCAGACTATTCCAGAAGATTTGGACCTACGAGA
TGATAGTCTGCTTAAAAATTTAGATATTAGGTGCATAAGAAGCCTTAACGGTTGCCGGGTAACTGATGAGATTTTACATC
TAGTACCAAACATTGACAGCTTCAGGTTAACACTGAGAGCCATCAAATTATGGGCCAAATGCCACAACATCTATTCCAAT
ATATTGGGTTTCCTTGGAGGTGTTTCCTGGGCTATGCTAGTAGCAAGAACTTGCCAGCTTTACCCAAATGCAATAGCATC
CACTCTTGTGCGAAAATTTTTCTTGGTGTTTTCTGAGTGGGAATGGCCAAATCCAGTGTTGTTAAAAGAACCAGAAGAAC
GAAATCTTAACTTGCCTGTATGGGACCCAAGAGTGAATCCTAGTGACAGGTACCATCTTATGCCTATAATTACACCAGCA
TACCCACAGCAGAACTCCACGTACAATGTGTCTGTTTCGACCAGGATGGTCATGATTGAGGAGTTTAAACAAGGACTTGC
TATCACACATGAAATTCTGCTGAATAAGGCAGAATGGTCCAAACTTTTTGAAGCTCCAAGCTTTTTTCAAAAATACAAGC
ATTATATTGTACTTCTGGCAAGTGCGCCAACAGAGAAACAACATTTAGAGTGGGTGGGCTTGGTGGAATCAAAGATCCGA
ATCCTGGTTGGGAGCCTGGAAAAGAATGAGTTCATTACTCTGGCTCATGTGAATCCTCAGTCGTTTCCAGCACCAAAAGA
AACTGCTGACAAGGAAGAATTTCGTACTATGTGGGTGATCGGGTTAGTGTTGAAGAAGCCAGAAAACTCTGAAATTCTCA
GTATTGATCTCACCTATGATATTCAGTCTTTCACAGATACAGTGTACAGACAAGCAATAAATAGTAAGATGTTTGAGATG
GATATGAAGATTGCTGCAATGCATCTAAGAAGGAAGGAACTTCATCAGCTACTTCCAAATCATGTTCTTCAGAAAAAGGA
AACCCATTTAACAGAAAGTGTAAGGCTGACAGCTGTGACTGACAGCAGCCTTCTCTTGTCTATAGACAGTGAAAACAGCA
TGACTGCTCCTTCACCTACTGGCACTATGAAGACAGGTCCACTGACTGGAAACCCTCAGGGCAGAAACAGTCCTGCTCTG
GCTGTTATGGCAGCATCTGTGACCAACATACAGTTTCCTGATGTTTCCTTGCAGCATGTGAATCCCATAGAAAGCTCAGG
AATTGCACTGAGTGAAAGCATCCCTCAGATTCCCTCACAACCTACCATTTCACCACCACCTAAGCCTACAATGACCAGAG
TGGTTTCTTCGACACATCTGGTAAACCATCCATCTAGACCTTCAGGAAATACAGCAACGAACATACCCAATCCTATACTA
GGAGTCTAG

Alignment

ORF - retro_mmus_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 87.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFPVTTQGSQQTQPPQRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNN
          MPF.VTTQG.QQ..P.....GI.SPISLAAPK.TD..LTQKLIETL.PFGVFEEEEELQRRILIL.KLNN
Retrocopy MPFAVTTQGAQQPAPAPKQFGISSPISLAAPKDTDRELTQKLIETLQPFGVFEEEEELQRRILILQKLNN

Parental  LVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
          LVKEWIREISES.NLPQ.VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR.DFFTSFYDKLKLQ
Retrocopy LVKEWIREISESRNLPQAVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRNDFFTSFYDKLKLQ

Parental  EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
          EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
Retrocopy EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI

Parental  LHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
          LHLVPNID.FRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLV.KFFLVFS.WE
Retrocopy LHLVPNIDSFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWE

Parental  WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
          WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.E
Retrocopy WPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHE

Parental  ILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
          ILL.KAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
Retrocopy ILLNKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS

Parental  FPAPKESPDREEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFELDMKIAAMHVKR
          FPAPKE..D.EEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH..R
Retrocopy FPAPKETADKEEFRTMWVIGLVLKKPENSEILSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLRR

Parental  KQLHQLLPSHVLQKRKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPA
          K.LHQLLP.HVLQK...H.TE.V.LTA..DSSL.LS.DS.NSM..PSPT..MKT.PL...G..QGRNSPA
Retrocopy KELHQLLPNHVLQKKETHLTESVRLTAVTDSSLLLSIDSENSMTAPSPTGTMKTGPL--TGNPQGRNSPA

Parental  PAVTAASVTSIQASEVSVPQANSSESPGGPSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPSPRPSG
          .AV.AASVT.IQ...VS....N..ES.G...SESIPQ...QP.ISPPPKPT..RVVSST.LVN...RPSG
Retrocopy LAVMAASVTNIQFPDVSLQHVNPIESSGIALSESIPQIPSQPTISPPPKPTMTRVVSSTHLVNHPSRPSG

Parental  NTATKVPNPIVGV
          NTAT..PNPI.GV
Retrocopy NTATNIPNPILGV

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	0.33 RPM	108.61 RPM
SRP007412_cerebellum	0.52 RPM	113.59 RPM
SRP007412_heart	0.09 RPM	78.51 RPM
SRP007412_kidney	0.06 RPM	134.82 RPM
SRP007412_liver	0.11 RPM	95.63 RPM
SRP007412_testis	389.15 RPM	129.81 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_37 was not detected

EST

No EST(s) were mapped for retro_mmus_37 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_111581	992 libraries	72 libraries	2 libraries	0 libraries	6 libraries
TSS #2	TSS_111582	1018 libraries	48 libraries	2 libraries	1 library	3 libraries

The graphical summary, for retro_mmus_37 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_37 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
Macaca mulatta	retro_mmul_1675
Callithrix jacchus	retro_cjac_1763
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 20 parental genes, and 22 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,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895,
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,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,