RetrogeneDB ID: retro_mmus_2488

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:99615826..99616327(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nsmce1
• Ensembl ID: ENSMUSG00000030750
• Aliases: Nsmce1, 2510027N19Rik
• Description: non-SMC element 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914961]

Sequence

>retro_mmus_2488
AGACCCATTTATGCACTGGCGAATCTTGCTACAACTTCAGTTTCCAAAATGGCCAGGGATTTTGCAGAGAGAACAAGTTG
AATCTGTTTAAGAAAGGCTTAGGAACTAATTGTTTACTCAGAAACTGGCTTTGCTTCTTCTACAAACATTTTGAACGAAG
TTGATCAACTCAGAGGCAAAAAGATGAGGAAGCAGAAAGCAGGGAGGTGCTGCAGAAATTTGTGCAGGTGACAGATAGGG
GTGGGGCGGTCACCTTGCATGGCCAGGCTATCCCTGGAGATGGAGTGGTTCACCTGAGAGAGCTACCCAGATTTTGTGAA
GATATGCAACATCTGCCACAGCTTCCTCATCAAGGCTCAAAGCTGTGAGACATGTTGTATTAGGATGCATTTGCCTTGCA
TGGCCAAGTACTTCCAGGCCACCTCTGGACCACACTGCCCGCCCTGTAATGACTGGCCCCATGACATAGCAGGAGTCTTC
AACCCTGAGAAGGAGAGGGAG

Alignment

ORF - retro_mmus_2488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.1 %
• Parental protein coverage: 60.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPIYALVNLATTSVSKMATDFAENELDL-FRKALELIVDSETGFASSTNILNLVDQLKGKKMRKK-EAEQ
          RPIYAL.NLATTSVSKMA.DFAE.......RKA.ELIV.SETGFASSTNILN.VDQL.GKKMRK..E...
Retrocopy RPIYALANLATTSVSKMARDFAERTS*ICLRKA*ELIVYSETGFASSTNILNEVDQLRGKKMRKQ<ESRE

Parental  VLQKFVQSKWLIEKEGEFTLHGRAI-LEMEQFIRESYPDSVKMCNICHGLLIQGQSCETCGIRMHLPCVA
          VLQKFVQ........G..TLHG.AI.LEME.F..ESYPD.VK.CNICH..LI..QSCETC.IRMHLPC.A
Retrocopy VLQKFVQ---VTDRGGAVTLHGQAI>LEMEWFT*ESYPDFVKICNICHSFLIKAQSCETCCIRMHLPCMA

Parental  KYFQSIPEPHCPHCNDYWPHDIPEVYNPEKERE
          KYFQ....PHCP.CND.WPHDI..V.NPEKERE
Retrocopy KYFQATSGPHCPPCND-WPHDIAGVFNPEKERE

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	8.76 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	26.93 RPM
SRP007412_kidney	0.00 RPM	18.86 RPM
SRP007412_liver	0.00 RPM	9.37 RPM
SRP007412_testis	0.00 RPM	109.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2488 was not detected

EST

No EST(s) were mapped for retro_mmus_2488 retrocopy.

TSS

No TSS is located nearby retro_mmus_2488 retrocopy 5' end.

Lab

retro_mmus_2488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564, retro_mmus_2488 ,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732,