RetrogeneDB ID: retro_mmus_3237

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:121972729..121973663(-)
• Located in intron of: ENSMUSG00000092329

Retrocopy information

• Ensembl ID: ENSMUSG00000091952
• 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_3237
AGGTTGGTTCTGCGGATTGCCACTGATGATTCCAAAGCCGTCTGTCGCCTCAGTGTTAAGTTTGGTGCCACACTCAAAAC
CAGCAGGCTTCTCTTGGAACGGGCAAAAGAGCTAAATATTGACGTCATTGGTGTGAGCTTCCATGTGGGCAGTGGATGTA
CTGACCCCGAGACCTTCGTTCAGGCAGTGTCGGATGCCCGCTGTGTGTTTGACATGGCAACAGAAGTCGGTTTCAGCATG
TATCTGCTTGATATTGGTGGTGGCTTTCCTGGATCTGAAGATACAAAACTTAAATTTGAAGAGATCACCAGTGTAATCAA
CCCAGCTCTGGACAAGTACTTCCCATCAGACTCTGGAGTGAGAATCATAGCTGAGCCAGGCAGATACTATGTCGCATCAG
CTTTCACGCTTGCAGTCAACATCATTGCCAAAAAAACCGTGTGGAAGGAGCAGCCCGGCTCTGATGATGAAGATGAGTCA
AATGAGCAAACCTTCATGTATTATGTGAATGATGGAATATATGGATCATTTAACTGCATTCTTTATGATCATGCCCATGT
GAAGGCCCTGCTGCAGAAGAGACCCAAGCCAGATGAAGTATTACTCATCCAGCATTTGGGGACCAACATGTGATGGCCTT
GATCGGATTGTGGAGCGCTGTAATCTGCCTGAAATGCATGTGGGTGATTGGATGCTGTTTGAGGACATGGGTGCATGCAC
CGTTGCTGCTGCTTCTACTTTCAATGGGTTCCAGAGGCCAAACATCTACTATGTAATGTCACGGCCAATGTGGCAACTCA
TGAAACAGATCCAGAGCCATGGCTTCCCGCCGGAGGTGGAGGAGCAGGATGATGGCACGCTGCCCATGTCTTGTGCCCAG
GAGAGCGGGATGGACTGTCACCCTGCAGCCTGTGCTTCTGCTAGGATCAATGTG

Alignment

ORF - retro_mmus_3237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.81 %
• Parental protein coverage: 67.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQAVSDARCVF
          .LVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQAVSDARCVF
Retrocopy RLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQAVSDARCVF

Parental  DMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVN
          DMATEVGFSM.LLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVN
Retrocopy DMATEVGFSMYLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVN

Parental  IIAKKTVWKEQPGSDDEDESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDE-KYYSSSIWGP
          IIAKKTVWKEQPGSDDEDESNEQTFMYYVNDG.YGSFNCILYDHAHVKALLQKRPKPDE..Y.SS.IWGP
Retrocopy IIAKKTVWKEQPGSDDEDESNEQTFMYYVNDGIYGSFNCILYDHAHVKALLQKRPKPDE>YYSSS-IWGP

Parental  TCDGLDRIVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMKQIQSHGFPPE
          TCDGLDRIVERCNLPEMHVGDWMLFE.MGA.TVAAASTFNGFQRPNIYYVMSRPMWQLMKQIQSHGFPPE
Retrocopy TCDGLDRIVERCNLPEMHVGDWMLFEDMGACTVAAASTFNGFQRPNIYYVMSRPMWQLMKQIQSHGFPPE

Parental  VEEQDDGTLPMSCAQESGMDRHPAACASARINV
          VEEQDDGTLPMSCAQESGMD.HPAACASARINV
Retrocopy VEEQDDGTLPMSCAQESGMDCHPAACASARINV

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	1.38 RPM	36.54 RPM
SRP007412_cerebellum	0.87 RPM	43.94 RPM
SRP007412_heart	0.47 RPM	40.72 RPM
SRP007412_kidney	0.50 RPM	253.38 RPM
SRP007412_liver	0.33 RPM	51.94 RPM
SRP007412_testis	0.18 RPM	221.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3237 was not detected

EST

No EST(s) were mapped for retro_mmus_3237 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_139884	241 libraries	324 libraries	451 libraries	42 libraries	14 libraries

The graphical summary, for retro_mmus_3237 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_3237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3237 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,