RetrogeneDB ID: retro_mmus_2502

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:112978485..112979813(-)
• Located in intron of: ENSMUSG00000087194

Retrocopy information

• Ensembl ID: ENSMUSG00000082678
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Minpp1
• Ensembl ID: ENSMUSG00000024896
• Aliases: Minpp1, AA408516
• Description: multiple inositol polyphosphate histidine phosphatase 1 [Source:MGI Symbol;Acc:MGI:1336159]

Sequence

>retro_mmus_2502
CCAGGGCGCGGCGACCCGGTGGCTTCGGTGCTCAGCCCCTTCTTCGGCACGAAGACACGCTACGAAGATGCCAATCCCTG
GCTGCTGGTCGATCCGGTGGCGCCGCGGCGGGACCCGGAGCTGCTGGCGGGGACCTGCACCCCGGTGCAGCTGGTCGCCC
TCATCCGTCACGGCACCCGCTACCCTACCACCAAGCAGATCCGCAAGCTGAAGCAGCTGCAGGGGCTGCTGCAGACCCGC
GAGTCCCGGGATGGCGGGAGCCAAGTGGCCGCCGCGCTGGCCGAATGGCCGCTGTGATATGGTGACTGGATGGACGGGCA
GCTGGTGGAGAAGGGGCGGCAGGACATGCGACAGCTGGCCCTGCGTCTGGCTGCCCTCTTCCCAGACCTCTTCAGCCGGG
AGAACTACGACCACCTGCGGCTGATCACCAGCTTCAAGCACCGCTGTGTGGACAGCAGCGCCGCCTTCCTCCAGGGGTTG
TGGCAGCATTACCACCCAGGACTGCCACCTCCCGACGTCTCAGATATGGAGTGTGACCCTCCAAGAATTAATGATAAACT
AATGAGGTTCTTCGATCATTGTGAGAAGTTCTTAACTGATGTGGAAAGAAACGCGACGGCTCTTTATCATGTAGAAGCTT
TCAAAACTGGACCAGAAATGCAGAAGGTCTTACAAAAAGTTGCAGCTACTCTGCAAGTTCCAGTGAACAGTTTAAATACA
GACTTAATTCAGGTAGCTTTTTTCACCTGTTCATTTGGCCTGGCAATTAAAGGTGTCCATTCTCCCTGGTTTGATGTGTT
TGACGTAGATGATGCAAGGGTTCTGGAATACTTAAACGACCTGAAACAGTACTGGAAACCAAGTTATGGCTACACCATTA
ACATCGGTCCAGCTGCAACCTATTTCAGGACATTTTTCTACACCTGGACAAAGCAGTGGAGCAGAAGCAAAGGTCTCAGC
TGGTCTCCTCTCCAGTCATCCTCCAGTTTCGACACGCGGAGACGCTCCTGCCGCTCCTCTCCCTCATGGGCTACTTCAAG
GACAAGGAGCCTCTGACCGCTTACAATTTCGAGGAGCAAGTTAACCACAAGTTCCGAAGTGGTCACATCGTACCTTACGT
CTCAAACCTAATCTTCGTGCTTTACCACTGTGACAACGCGCAGAGCCCCGAAGAACAATTCCAGATACAGCCGCTGCTGA
ATGAGAAGGTGCTGCCCCTGGCTCACTCGCAGAGACCTGTCAGGTTGTATGAGGAGCTCAAGACCCACTACCGGGACATT
CTTCAGAGCTGCCAAACTAGTAAGGAGTGCAGCCCGCCCAAAGTGAAC

Alignment

ORF - retro_mmus_2502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 92.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGRGDPVASVLSPYFGTKTRYEDANPWLLVDPVAPRRDPELLAGTCTPVQLVALIRHGTRYPTTKQIRKL
          PGRGDPVASVLSP.FGTKTRYEDANPWLLVDPVAPRRDPELLAGTCTPVQLVALIRHGTRYPTTKQIRKL
Retrocopy PGRGDPVASVLSPFFGTKTRYEDANPWLLVDPVAPRRDPELLAGTCTPVQLVALIRHGTRYPTTKQIRKL

Parental  KQLQGLLQTRESRDGGSQVAAALAEWPLWYGDWMDGQLVEKGRQDMRQLALRLAALFPDLFSRENYDRLR
          KQLQGLLQTRESRDGGSQVAAALAEWPL.YGDWMDGQLVEKGRQDMRQLALRLAALFPDLFSRENYD.LR
Retrocopy KQLQGLLQTRESRDGGSQVAAALAEWPL*YGDWMDGQLVEKGRQDMRQLALRLAALFPDLFSRENYDHLR

Parental  LITSSKHRCVDSSAAFLQGLWQHYHPGLPPPDVSDMECGPPRINDKLMRFFDHCEKFLTDVERNETALYH
          LITS.KHRCVDSSAAFLQGLWQHYHPGLPPPDVSDMEC.PPRINDKLMRFFDHCEKFLTDVERN.TALYH
Retrocopy LITSFKHRCVDSSAAFLQGLWQHYHPGLPPPDVSDMECDPPRINDKLMRFFDHCEKFLTDVERNATALYH

Parental  VEAFKTGPEMQKVLKKVAATLQVPMNSLNADLIQVAFFTCSFDLAIKGVHSPWCDVFDVDDARVLEYLND
          VEAFKTGPEMQKVL.KVAATLQVP.NSLN.DLIQVAFFTCSF.LAIKGVHSPW.DVFDVDDARVLEYLND
Retrocopy VEAFKTGPEMQKVLQKVAATLQVPVNSLNTDLIQVAFFTCSFGLAIKGVHSPWFDVFDVDDARVLEYLND

Parental  LKQYWKRSYGYTIN-SRSSCNLFQDIFLHLDKAVEQKQRSQPVSSPVILQFGHAETLLPLLSLMGYFKDK
          LKQYWK.SYGYTIN..RSSCNLFQDIFLHLDKAVEQKQRSQ.VSSPVILQF.HAETLLPLLSLMGYFKDK
Retrocopy LKQYWKPSYGYTIN<HRSSCNLFQDIFLHLDKAVEQKQRSQLVSSPVILQFRHAETLLPLLSLMGYFKDK

Parental  EPLTAYNFEEQVNRKFRSGHIVPYASNLIFVLYHCDNAQSPEEQFQIQLLLNEKVLPLAHSQRPVGLYEE
          EPLTAYNFEEQVN.KFRSGHIVPY.SNLIFVLYHCDNAQSPEEQFQIQ.LLNEKVLPLAHSQRPV.LYEE
Retrocopy EPLTAYNFEEQVNHKFRSGHIVPYVSNLIFVLYHCDNAQSPEEQFQIQPLLNEKVLPLAHSQRPVRLYEE

Parental  LKTHYRDILQSCQTSKECSPPKAN
          LKTHYRDILQSCQTSKECSPPK.N
Retrocopy LKTHYRDILQSCQTSKECSPPKVN

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	39.65 RPM
SRP007412_cerebellum	0.04 RPM	20.36 RPM
SRP007412_heart	0.00 RPM	9.09 RPM
SRP007412_kidney	0.02 RPM	28.49 RPM
SRP007412_liver	0.00 RPM	24.09 RPM
SRP007412_testis	0.00 RPM	10.84 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2502 was not detected

EST

No EST(s) were mapped for retro_mmus_2502 retrocopy.

TSS

No TSS is located nearby retro_mmus_2502 retrocopy 5' end.

Lab

retro_mmus_2502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2502 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013275	4 retrocopies	retro_chof_1750, retro_chof_387, retro_chof_786, retro_chof_796,
Mus musculus	ENSMUSG00000024896	1 retrocopy	retro_mmus_2502 ,
Oryctolagus cuniculus	ENSOCUG00000002908	1 retrocopy	retro_ocun_1283,
Rattus norvegicus	ENSRNOG00000011287	1 retrocopy	retro_rnor_32,