RetrogeneDB ID: retro_mmus_2922

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:41490350..41491640(+)
• Located in intron of: ENSMUSG00000074166

Retrocopy information

• Ensembl ID: ENSMUSG00000083500
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2922
ATGAGCAGCTTTACTAAGGAAGAGTTTGACTGCCACATCCTCGATGAAGGCTTTACTGCCTAGGACACTCTGAACCAACA
AATCAATGAAGTCTCTTCCTCTGACGATAAGGATGCGTTCTATGTTGCGGACCTCGGAGACATTCTTAAGCATCTGAGGT
GGCTAAAAGCTCCTCCCCGTGTTACTCCCTTTTACGCAGTCAAATGTAACGATAGCAGAGCCATAGTGAGCACCCTAGCT
GCCATTGGGACAGGATTTGACTGTGCAAGCAAGACTGAAATACAGTTGGTACAGGGGCCTGGGGTGCCTGCAGAGAGGAT
TATCTATGCAAATCCTTGTAAACAAGTCTCTCAAATCAAGTATGCTGCCAGTAACGGAGTCCAGATGATGACTTTTGACA
GAGAAATTGAATTGATGAAAGTCGCCAGAGCACATCCAAAGGCAAAGTTGGTTCTGCGGATTGCCACTGATGATTCCAAA
GCAGTGTGCTGCCTCAGTGTTAAGTTTGGTGCCACACTCAAAACCAGCAGGCTTCTCTTGGAACGGGCAAAAGAGCTAAA
TATTGACGTCATTGGTGCGAGCTTCCATGTGAGCAGTGGATGTACTGACCCCGATACCTTCGTGCAGGCAGTGTCTGATG
CCCGCTGTGTGTTTGACATGGGAACAGAAGTTGGTTTCAGCATGCATCTGCTTGATATTGGTGGTGGCTTTCCTGGATCT
GAAGATACAACATTTATATTTGAAGAGATCACCAGTGTAATCAACCCAGCTCTGGACAAGTACTTCCCATCAGACTCTGG
AGTGAGAATCATAGCTGAGCCAGGCAGATACTATGTCACATCAGCTTTCACGCTTGCAGTCAACATCATTGCCAAAAAAA
GTGTGGAAAGAACAGTCCAGCTCTGATGATGAAGATGACTCAAATAAGTAAACCTTCATGTATCATGTGAATGATGGAGT
ATATGGATCATTTAACTGCATTCTTTATGATCATGCCCATGTGAAGGCCCTGCTGCAGAAGAGACCCAAGCCAGATGAGA
AGTATTACTCATCCAGCATCTGGGGACCAACATCTGATGGCCTTGATCAGATCGTTGAGCGCTGTAACCTGCCTGAAATG
AATGTGGGTGATTGGATGCTGTTTGAGAACATGGGTGCATACACCATTGCTGCTGCTTCTACTTTCAATGGGTTCCAATG
GCCAAACAACTACTATGTAATGTCATGGCCAAAGTGGCAACTCATGAAGCAGATCCAGATGCATGGCTTGCCATGGAAGT
AGAGGAACAG

Alignment

ORF - retro_mmus_2922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 93.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSFTKDEFDCHILDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKC
          MSSFTK.EFDCHILDEGFTA.D.L.Q.INEVSSSDDKDAFYVADLGDILK.HLRWLKA.PRVTPFYAVKC
Retrocopy MSSFTKEEFDCHILDEGFTA*DTLNQQINEVSSSDDKDAFYVADLGDILK-HLRWLKAPPRVTPFYAVKC

Parental  NDSRAIVSTLAAIGTGFDCASKTEIQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELM
          NDSRAIVSTLAAIGTGFDCASKTEIQLVQG.GVPAER.IYANPCKQVSQIKYAASNGVQMMTFD.EIELM
Retrocopy NDSRAIVSTLAAIGTGFDCASKTEIQLVQGPGVPAERIIYANPCKQVSQIKYAASNGVQMMTFDREIELM

Parental  KVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQ
          KVARAHPKAKLVLRIATDDSKAVC.LSVKFGATLKTSRLLLERAKELNIDVIG.SFHV.SGCTDP.TFVQ
Retrocopy KVARAHPKAKLVLRIATDDSKAVCCLSVKFGATLKTSRLLLERAKELNIDVIGASFHVSSGCTDPDTFVQ

Parental  AVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYV
          AVSDARCVFDM.TEVGFSMHLLDIGGGFPGSEDT...FEEITSVINPALDKYFPSDSGVRIIAEPGRYYV
Retrocopy AVSDARCVFDMGTEVGFSMHLLDIGGGFPGSEDTTFIFEEITSVINPALDKYFPSDSGVRIIAEPGRYYV

Parental  ASAFTLAVNIIAKKTV-WKEQP-GSDDEDESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDE
          .SAFTLAVNIIAKK.V..K..P..SDDED.SN..TFMY.VNDGVYGSFNCILYDHAHVKALLQKRPKPDE
Retrocopy TSAFTLAVNIIAKKSV<GKNSP<SSDDEDDSNK*TFMYHVNDGVYGSFNCILYDHAHVKALLQKRPKPDE

Parental  KYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMK
          KYYSSSIWGPT.DGLD.IVERCNLPEM.VGDWMLFENMGAYT.AAASTFNGFQ.PN.YYVMS.P.WQLMK
Retrocopy KYYSSSIWGPTSDGLDQIVERCNLPEMNVGDWMLFENMGAYTIAAASTFNGFQWPNNYYVMSWPKWQLMK

Parental  QIQSHGFP-PEVEEQ
          QIQ.HG.P..EVEEQ
Retrocopy QIQMHGLP<MEVEEQ

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	0.84 RPM	36.54 RPM
SRP007412_cerebellum	0.74 RPM	43.94 RPM
SRP007412_heart	0.44 RPM	40.72 RPM
SRP007412_kidney	0.87 RPM	253.38 RPM
SRP007412_liver	0.52 RPM	51.94 RPM
SRP007412_testis	0.32 RPM	221.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2922 was not detected

EST

No EST(s) were mapped for retro_mmus_2922 retrocopy.

TSS

No TSS is located nearby retro_mmus_2922 retrocopy 5' end.

Lab

retro_mmus_2922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2922 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,