RetrogeneDB ID: retro_mmus_2746

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:70437196..70438303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Odc1
• Ensembl ID: ENSMUSG00000011179
• Aliases: Odc1, ODC
• Description: ornithine decarboxylase, structural 1 [Source:MGI Symbol;Acc:MGI:97402]

Sequence

>retro_mmus_2746
AATGAAGTATCTTCTTTCTATGTTGTGGACCTCAGAGACATTCTAAAGAAGCATCTGAGGTGGCTAAAAGGTCTTCCCTG
TGTTATTCACTTTTGTGCAGTCAAGTGTAAGGACAACAGAGTCATAGTGATCACCCTAGCTGCTATTGGGACAGGATTTG
ACTGTGTAAGCAAGACTGAAATACAGTTGGTGCAGGGGCTTCTGGTGCCTCCAGAGAGGATTACCTTGCACATCTTTGTA
AACACATGTCTCAAATCAAGTATACTTGCCAGTAATGCAGTCCATATGATGACTTTCAACAGTGAAATTGAATTGATGAA
AGTCGTCAGAGCACATCGAAAGACAAAGTTGGTTGTGTGGATTGTCACTGATGATTCCAAAGCAGTTTGTCGACTTGGTG
TTAAGTCTGGTGCCACACTCAAAATCAGCAGGCTCCTCCTGAAATGGGATAAAAGAGCTAAATATTGACGTCATTGATGT
CAGCTTCCATGTGTGCAGTGGAGGTATTGACCTGAGACCTTCATGCAGGCAGTGTCAGATGCCCACTGTGTATTTGACCT
GGGAACAGAAGTTGGTTTCAGCATGTATCTGTTTGATATTGGTGGTGGCTTTCCTGGATCTGAAGATACAAAGCTTAAAT
TTGAAGAGGTCACCAGTGTGATCAACCCAGCTCTGGACAAGTACTTCCCATCAGACTCTGGAATGAGAATCACAGCTGAG
CTGGGCAGATACTATGCTTAGCTTTCATACTTGCAGTCAATATCATTGCCTGCCCCCCCCCCAAAAAAAGGTAGGAAGAG
CCGACCTGCTCTGACTATGAAGATAAGCAAGCCTTCATGCATTATGTGAATGATGGAGTGTATGTATCATTTAACTGCAT
TCTTTATGATCATGCACATGTGAAGGCCCTGCTGCAGGAGACCCAAGCCAGATGAGAAGTATTACTAATCCAGCATCTGG
GAGCCAACATGTGATGGCCTTGAACCAATTGTTGGGCACTGTAATCTGCCTGAAATGCATGTGGGTAATTGGATGCTGTT
TGGGAATATGGGTGAATTCACCATTGCTGTTGCTTCTTCTTTCAATGGGGTCCAGAGGCCAAACATC

Alignment

ORF - retro_mmus_2746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.09 %
• Parental protein coverage: 80.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEIQLVQGLGVP
          .....FYV.DL.DILKKHLRWLK.LP.V..F.AVKC.D.R.IV.TLAAIGTGFDC.SKTEIQLVQGL.VP
Retrocopy NEVSSFYVVDLRDILKKHLRWLKGLPCVIHFCAVKCKDNRVIVITLAAIGTGFDCVSKTEIQLVQGLLVP

Parental  AERVIY-ANPCKQVSQIKYA-ASNGVQMMTFDSEIELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGA
          .ER....A..CK..SQIKY..ASN.V.MMTF.SEIELMKV.RAH.K.KLV..I.TDDSKAVCRL.VK.GA
Retrocopy PERITL<AHLCKHMSQIKYT>ASNAVHMMTFNSEIELMKVVRAHRKTKLVVWIVTDDSKAVCRLGVKSGA

Parental  TLKTSRLLLE-RAKELNIDVIGVSFHVGSGCTD-PETFVQAVSDARCVFDMATEVGFSMHLLDIGGGFPG
          TLK.SRLLL....KELNIDVI.VSFHV.SG..D.PETF.QAVSDA.CVFD..TEVGFSM.L.DIGGGFPG
Retrocopy TLKISRLLLK>GIKELNIDVIDVSFHVCSGGID<PETFMQAVSDAHCVFDLGTEVGFSMYLFDIGGGFPG

Parental  SEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVA-SAFTLAVNIIAKKTVWKEQPGSDDEDES
          SEDTKLKFEE.TSVINPALDKYFPSDSG.RI.AE.GR.Y.A..AF.LAVNIIA.....K........D..
Retrocopy SEDTKLKFEEVTSVINPALDKYFPSDSGMRITAELGR-YYA<LAFILAVNIIAXXXXKKR*EEPTCSDYE

Parental  NEQTFMYYVNDGVYGSFNCILYDHAHVKALLQ-KRPKPDEKYYSSSIWGPTCDGLDRIVERCNLPEMHVG
          ..Q.FM.YVNDGVY.SFNCILYDHAHVKALLQ.........Y.SS.IW.PTCDGL..IV..CNLPEMHVG
Retrocopy DKQAFMHYVNDGVYVSFNCILYDHAHVKALLQ>RPKPDEKYY*SS-IWEPTCDGLEPIVGHCNLPEMHVG

Parental  DWMLFENMGAYTVAAASTFNGFQRPNI
          .WMLF.NMG..T.A.AS.FNG.QRPNI
Retrocopy NWMLFGNMGEFTIAVASSFNGVQRPNI

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	0.02 RPM	36.54 RPM
SRP007412_cerebellum	0.00 RPM	43.94 RPM
SRP007412_heart	0.00 RPM	40.72 RPM
SRP007412_kidney	0.02 RPM	253.38 RPM
SRP007412_liver	0.00 RPM	51.94 RPM
SRP007412_testis	0.00 RPM	221.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2746 was not detected

EST

No EST(s) were mapped for retro_mmus_2746 retrocopy.

TSS

No TSS is located nearby retro_mmus_2746 retrocopy 5' end.

Lab

retro_mmus_2746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2746 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746 , retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,