RetrogeneDB ID: retro_mmus_2558

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:32420084..32420969(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000097978
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdlim1
• Ensembl ID: ENSMUSG00000055044
• Aliases: None
• Description: PDZ and LIM domain 1 (elfin) [Source:MGI Symbol;Acc:MGI:1860611]

Sequence

>retro_mmus_2558
GTCACTCCCGGAAGCAAGGCTGCTATAGCGAATTTATGTATTGGAGATTTAATCACAGCCATCGATGGGGAAGGTACCAG
CAGCATGACACACTTGGAAGCTCAGAACAAAATCAAGGGCTGCGCAGACAACATGACGCTCACAGTATCCAGGTCTGAAC
AGAAGATTTGGTCTCCTCTAGTGACTGAGGAGGGGAAACGTCATCCCTACAAGATGAATTTAGCGTCGGAACCCCAAGAA
GTCCTGCACATAGGAAGTGCCCACAACCGAAGTGCCATGCCATTTACTGCCTCACCTGCTCCCAGCACCCGGGTCATCAC
AAACCAGTACAACAGCCCAACTGACCTCTACTCATCCGAAAACATCTCTAACTTCAACAATGCTGTGGAGTCGAAGACCT
CAGCCAGTGGGAAGGAGGCGAACAGCAGGCCCTTGGTTCAGCCTCATCCCTCTGGCAGCCTTATCATTGACAAGGAATCT
GAAGTTTACAAGATGCTTCAGGAGAAGCAAGAATTAAACGAGCCCCCCAAACAGTCCACATCCTTCCTGGTTCTGCAGGA
GATCCTGGAGTCAGATGGGAAAGGGGATCCCAACAAGCCATCAGGATTTAGAAGTGTTAAAGCTCCAGTCACCAAAGTGG
CTGCATCTGTTGGAAATGCTCAGAAGCTGCCCATCTGTGACAAATGTGGAACTGGTATTGTTGGTGTGTTTGTGAAGCTG
AGGGATCACCATCGCCACCCTGAATGCTATGTGTGCACCGACTGTGGCATCAACCTGAAACAGAAGGGCCATTTCTTTGT
AGAGGATCAGATTTACTGTGAAAAGCACGCCAGGGAGCGGGTCACACTGCCTGAGGGCTATGATGTGGTCACAGTGTTCC
GCAAG

Alignment

ORF - retro_mmus_2558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.63 %
• Parental protein coverage: 90.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTPGSKAAIANLCIGDLITAIDGEDTSSMTHLEAQNKIKGCADNMTLTVSRSEQKIWSPLVTEEGKRHPY
          VTPGSKAAIANLCIGDLITAIDGE.TSSMTHLEAQNKIKGCADNMTLTVSRSEQKIWSPLVTEEGKRHPY
Retrocopy VTPGSKAAIANLCIGDLITAIDGEGTSSMTHLEAQNKIKGCADNMTLTVSRSEQKIWSPLVTEEGKRHPY

Parental  KMNLASEPQEVLHIGSAHNRSAMPFTASPAPSTRVITNQYNSPTGLYSSENISNFNNAVESKTSASGEEA
          KMNLASEPQEVLHIGSAHNRSAMPFTASPAPSTRVITNQYNSPT.LYSSENISNFNNAVESKTSASG.EA
Retrocopy KMNLASEPQEVLHIGSAHNRSAMPFTASPAPSTRVITNQYNSPTDLYSSENISNFNNAVESKTSASGKEA

Parental  NSRPVVQPHPSGSLIIDKDSEVYKMLQEKQELNEPPKQSTSFLVLQEILESDGKGDPNKPSGFRSVKAPV
          NSRP.VQPHPSGSLIIDK.SEVYKMLQEKQELNEPPKQSTSFLVLQEILESDGKGDPNKPSGFRSVKAPV
Retrocopy NSRPLVQPHPSGSLIIDKESEVYKMLQEKQELNEPPKQSTSFLVLQEILESDGKGDPNKPSGFRSVKAPV

Parental  TKVAASVGNAQKLPICDKCGTGIVGVFVKLRDHHRHPECYVCTDCGINLKQKGHFFVEDQIYCEKHARER
          TKVAASVGNAQKLPICDKCGTGIVGVFVKLRDHHRHPECYVCTDCGINLKQKGHFFVEDQIYCEKHARER
Retrocopy TKVAASVGNAQKLPICDKCGTGIVGVFVKLRDHHRHPECYVCTDCGINLKQKGHFFVEDQIYCEKHARER

Parental  VTPPEGYDVVTVFRE
          VT.PEGYDVVTVFR.
Retrocopy VTLPEGYDVVTVFRK

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	0.00 RPM	4.67 RPM
SRP007412_cerebellum	0.00 RPM	3.99 RPM
SRP007412_heart	0.19 RPM	38.73 RPM
SRP007412_kidney	0.04 RPM	10.16 RPM
SRP007412_liver	0.03 RPM	24.80 RPM
SRP007412_testis	0.14 RPM	3.02 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2558 was not detected

EST

1 EST(s) were mapped to retro_mmus_2558 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI048045	32420558	32420775	99.6	215	1	213

TSS

No TSS is located nearby retro_mmus_2558 retrocopy 5' end.

Lab

retro_mmus_2558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558 , retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,