RetrogeneDB ID: retro_mmus_2897

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:13178902..13180171(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048261
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wdr12
• Ensembl ID: ENSMUSG00000026019
• Aliases: Wdr12, 4933402C23Rik, Ytm1, Ytm1p
• Description: WD repeat domain 12 [Source:MGI Symbol;Acc:MGI:1927241]

Sequence

>retro_mmus_2897
ATGGCACAACTCCAGGCACGTTTCTACAGCGAGAACAAGAAATACGCAGTGGATGATGTCCCTTTCTCAATCCCTGCCGC
TGCTGAAGTTGCCGACCTTAGTAACATTATCAATAAGTTGCTGGAGACCAAAAATGAACTCCACAAACATGTCGAGTTTG
ATTTCCTTATCAAGAGCCAGTTTCTTCGAGTGCCCTTGGTCAAACACACGGAACTGGAGAACATTTCATCGGAAGAGGTT
GTGGAACTAGAATATGTGGAAAAGTACACCGCACCCCAGCCAAAGCAGTGCATGTTCCATGATGACTGGATCAGCTCAAT
TAAAGGGGCAGAAGAATGGATCCTGTCTGGTTCGTATGATAAGACTTCTCAAATCTGGTCCTTGGAAGGAAAGTCAGTAA
TGACAATTGTGGGACATACAGATGTTGTGAAAGATGTGGCTTGGGTGAAAAAAGACAGTTTGTTCTGCTTACTACTGACG
GCCTCGATGGACCAGACTGTTCTCTTATGGGAGTGGAATGTAGAGAAGAACAAAGTGAAAGCTCTGCACTGCTGCCAAGG
GCATGCTGGGAGTGTGGGCGCCATCGCAGTCGATAGCTCGGGAGCTAAGTTTTGCAGTGCCTCCTGGGATAAGATGCTAA
AGATCTGGTCTACAGTCCCTACAGATGAAGAAGATGAAATGGAAGAAGCCACAAATCGTCCAAGAAAAAAGCAAAAACCA
GAACAATTGGGACTAACAAGAACACCCTTGGTGACCCTCTCTTGCCACACAGAAGCAATTTCCTCAGTCCTTTGGTCAGA
TGCTGAAGAAATCTGTAGTGCATCTTGGGATCACACAATTAGAGTGTGGGATGTTGAGTCTGGCGGTCTTAAGTCAACTC
TGACAGGAAATAAAGTGTTTAATTGTATTTCCTATTCTCCCCTTTGTAAACGTTTGACATCTGGAAGCACAGACAGGCAT
ATTAGACTGTGGGATCCCCGAACTAAAGATGGTTTTTTGGTGTCGCTGTCTCTCACCTCACACACAGGCTGGGTGACATC
AGTGAAATGGTTTCCTACCCATGAACAACAGCTGATCTCGGGCTCTTTAGATAACATTGTGAAGCTATGGGATGCAAGAA
GCTGTAAGGCTCCTCTCTATGATCTAGCTGCTCATGAAGACAAAGTTCTAAGTGTGGACTGGACAGACACAGGGCTACTT
CTGAGTGGAGGAGCAGACAATAAATTGTATTCCTACAGATATTCCCCTACCACTTCCCATGTTGGGGCT

Alignment

ORF - retro_mmus_2897 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQLQARFYSENKKYAVDDVPFSIPAAAEVADLSNIINKLLETKNELHKHVEFDFLIKGQFLRVPLVKHM
          MAQLQARFYSENKKYAVDDVPFSIPAAAEVADLSNIINKLLETKNELHKHVEFDFLIK.QFLRVPLVKH.
Retrocopy MAQLQARFYSENKKYAVDDVPFSIPAAAEVADLSNIINKLLETKNELHKHVEFDFLIKSQFLRVPLVKHT

Parental  ELENISSEEVVELEYVEKYTAPQPEQCMFHDDWISSIEGAEEWILSGSYDKTSRIWSLEGKSIMTIVGHT
          ELENISSEEVVELEYVEKYTAPQP.QCMFHDDWISSI.GAEEWILSGSYDKTS.IWSLEGKS.MTIVGHT
Retrocopy ELENISSEEVVELEYVEKYTAPQPKQCMFHDDWISSIKGAEEWILSGSYDKTSQIWSLEGKSVMTIVGHT

Parental  DVVKDVAWVKKDSLSCLLLTASMDQTVLLWEWNVEKNKVKALHCCRGHAGSVDAIAVDSSGAKFCSGSWD
          DVVKDVAWVKKDSL.CLLLTASMDQTVLLWEWNVEKNKVKALHCC.GHAGSV.AIAVDSSGAKFCS.SWD
Retrocopy DVVKDVAWVKKDSLFCLLLTASMDQTVLLWEWNVEKNKVKALHCCQGHAGSVGAIAVDSSGAKFCSASWD

Parental  KMLKIWSTVPTDEEDEMEEATNRPRKKQKTEQLGLTRTPLVTLSGHTEAISSVLWSDAEEICSASWDHTI
          KMLKIWSTVPTDEEDEMEEATNRPRKKQK.EQLGLTRTPLVTLS.HTEAISSVLWSDAEEICSASWDHTI
Retrocopy KMLKIWSTVPTDEEDEMEEATNRPRKKQKPEQLGLTRTPLVTLSCHTEAISSVLWSDAEEICSASWDHTI

Parental  RVWDVESGGLKSTLTGNKVFNCISYSPLCKRLASGSTDRHIRLWDPRTKDGSLVSLSLTSHTGWVTSVKW
          RVWDVESGGLKSTLTGNKVFNCISYSPLCKRL.SGSTDRHIRLWDPRTKDG.LVSLSLTSHTGWVTSVKW
Retrocopy RVWDVESGGLKSTLTGNKVFNCISYSPLCKRLTSGSTDRHIRLWDPRTKDGFLVSLSLTSHTGWVTSVKW

Parental  SPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDKVLSVDWTDTGLLLSGGADNKLYSYSYSPTTSH
          .PTHEQQLISGSLDNIVKLWD.RSCKAPLYDLAAHEDKVLSVDWTDTGLLLSGGADNKLYSY.YSPTTSH
Retrocopy FPTHEQQLISGSLDNIVKLWDARSCKAPLYDLAAHEDKVLSVDWTDTGLLLSGGADNKLYSYRYSPTTSH

Parental  VGA
          VGA
Retrocopy VGA

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	26.05 RPM
SRP007412_cerebellum	0.00 RPM	20.19 RPM
SRP007412_heart	0.03 RPM	11.02 RPM
SRP007412_kidney	0.04 RPM	12.32 RPM
SRP007412_liver	0.03 RPM	11.55 RPM
SRP007412_testis	0.27 RPM	111.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2897 was not detected

EST

1 EST(s) were mapped to retro_mmus_2897 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV326968	13179483	13179658	95	114	6	107

TSS

No TSS is located nearby retro_mmus_2897 retrocopy 5' end.

Lab

retro_mmus_2897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897 ,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,