RetrogeneDB ID: retro_mmus_503

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:152729683..152730559(-)
• Located in intron of: ENSMUSG00000026482

Retrocopy information

• Ensembl ID: ENSMUSG00000080950
• 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_503
ATGAGCAGCTTTACTAAGGACGAGTTTGACTGCCACATCCTTGATGAAGGCTTTACTGCTAAGGACATTCTGGACCAAAA
AAATCAATGAAGTCTCTTCCTCTGACGATAAGGATGCGTCTATGTTGCGGACCGCGGAGACATTCTAAAGAAGCAGCAGA
GGTGGCTAGAAGCTCTTCCCCGAGTTACTCCCTTTTACGCAGTCAAGTGTAAAGATAGCAGAGCCATAGTGAGCACCCTA
GCTGCCATTGGGACAGGATTTGACTGTGCAAGCAAGACTGAAATACAGTTGGTGCAGGGGCCTGGGGTGCCTGCAGAGAG
GATTATCTATGTAAATCCTTGTAAGCCAGTCTCTCAAATCAAGTACGCTGCCAGTAGCGGAGTCCAGATGATGACTTTTG
ACAGTGAAATTGAATTGATGAAAGTCGCCAGAGCACATCCAAAGGCAAAGTTGGTTCTGCGGATTGCCACTGATGATTCC
AAAGCAGCGTGCCGCCTCAGTGTTAAGTTTGGTGCCACACTCAAAACCAGCAGGCTTCTCTTGGAACGGGCAAAAGAGCT
AAATATTGACGTCATTGGTATGAGCTTCCATGTGGGCAGTGGATGTACTGACCCCGAGACCTTCGTGCAGGCAGTGTCGA
ATGCCCGCTGTGTGTTTGACATGGGAACAGAAGTTGGTTTCAGCATGTATCTGCTTGATATTGGTGGTGGCTTTCCTAGA
TCTGAAGATACAAAGCTTAAATTTGAAGAGATCACCAGTGTAATCAACCCAGCTCTGGACAAGTACTTCCCATCAGACTC
TGGAGTGAGAATCATAGCTGAGCCAGGCAGATACTATGTCGCGTCAGCTTTCACGCCTGCAGTCAACATCATTGCC

Alignment

ORF - retro_mmus_503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 63.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSFTKDEFDCHILDEGFTAKDILDQK-INEVSSSDDKDA-FYVADLGDILKKHLRWLKALPRVTPFYAV
          MSSFTKDEFDCHILDEGFTAKDILDQK.INEVSSSDDKDA..YVAD.GDILKK..RWL.ALPRVTPFYAV
Retrocopy MSSFTKDEFDCHILDEGFTAKDILDQK>INEVSSSDDKDA<VYVADRGDILKKQQRWLEALPRVTPFYAV

Parental  KCNDSRAIVSTLAAIGTGFDCASKTEIQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIE
          KC.DSRAIVSTLAAIGTGFDCASKTEIQLVQG.GVPAER.IY.NPCK.VSQIKYAAS.GVQMMTFDSEIE
Retrocopy KCKDSRAIVSTLAAIGTGFDCASKTEIQLVQGPGVPAERIIYVNPCKPVSQIKYAASSGVQMMTFDSEIE

Parental  LMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETF
          LMKVARAHPKAKLVLRIATDDSKA.CRLSVKFGATLKTSRLLLERAKELNIDVIG.SFHVGSGCTDPETF
Retrocopy LMKVARAHPKAKLVLRIATDDSKAACRLSVKFGATLKTSRLLLERAKELNIDVIGMSFHVGSGCTDPETF

Parental  VQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRY
          VQAVS.ARCVFDM.TEVGFSM.LLDIGGGFP.SEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRY
Retrocopy VQAVSNARCVFDMGTEVGFSMYLLDIGGGFPRSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRY

Parental  YVASAFTLAVNIIA
          YVASAFT.AVNIIA
Retrocopy YVASAFTPAVNIIA

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	0.26 RPM	36.54 RPM
SRP007412_cerebellum	0.04 RPM	43.94 RPM
SRP007412_heart	0.00 RPM	40.72 RPM
SRP007412_kidney	0.29 RPM	253.38 RPM
SRP007412_liver	0.03 RPM	51.94 RPM
SRP007412_testis	0.37 RPM	221.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_503 was not detected

EST

No EST(s) were mapped for retro_mmus_503 retrocopy.

TSS

No TSS is located nearby retro_mmus_503 retrocopy 5' end.

Lab

retro_mmus_503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_503 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,