RetrogeneDB ID: retro_mmus_3134

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:53911738..53912585(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Kansl2
• Ensembl ID: ENSMUSG00000022992
• Aliases: Kansl2, 2310037I24Rik, B930009D17
• Description: KAT8 regulatory NSL complex subunit 2 [Source:MGI Symbol;Acc:MGI:1916862]

Sequence

>retro_mmus_3134
GAAGACAACTGGAGTGATGGGGACCATGGACATTTTACTGTGGATCAGACATGGAGAGGTGAAGGTAAAAGGATAGACAG
TGATGGAGAAGGTCCCCTAACACATGCTGGTGTCTATGCAGCTGAAGAAGTGGCTCTTATTATGAAAGAAAAGCAAATTT
GTTTGCAATCTTTGTACACTGATCAGTTTCAGCGACTGCAACACCTGTTCAAAGAGAAGAAGCGCAGTTATTTACATAAT
CAAAAAGTGGAACAGGAAGCTTTAGGTAGTAGTCTCCCGACTGGCTCTGAGGGACTTTTGGCTAAAGAGAGAGAGAATTC
AAAGCAACTAAAATGTCTTAGGTGATGCTGTCAGCACAATGGAGCAGAAGCCTTAGTGCAAAGGCAGCTGAGGGAATGCA
GAATGATGGCCACACATGGGGCTGCTCACCAGGCTCGTACCACTCATTCCAGTCAGAGATGCTTAGCCTTTGTGGAAAAT
GTTCACTGCTCCAATCAGGCTCTTCTGATGAGCAGACACTTCCTTACCCATATCTGCCAGGATACAAATCAGGTTCTCTT
CAAATGTTGCCAGTGATCTGAAGAGGTACCCTGCAACAAACACAGTTCCTGTAAGCCTTTCTGAGGTTCCCTGCCGTCTG
TTGCATTTCCAGTTGTCTCTTCAAATCTATAAACCTGAGTAGGACTTGGGTGTTATGGGTGATGGTATGTCATAACCTCT
GTCGCCCTTGCTTTTCGACCCTTCACTAACTCTTGAAGATCATTCAGTCACAGAAACTGCCAGAGGCCCAGGGCAAATGC
AGTTGGTTGGGGCTGGGTGCAGATCCCAGGGACCTCGAAATATAGAG

Alignment

ORF - retro_mmus_3134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDSWSDGDQEPITVDQTWRGDPDSEADSIDSDQEDPLKHAGVYTAEEVALIMREKLIRLQSLYIDQFKRL
          ED.WSDGD....TVDQTWRG....E...IDSD.E.PL.HAGVY.AEEVALIM.EK.I.LQSLY.DQF.RL
Retrocopy EDNWSDGDHGHFTVDQTWRG----EGKRIDSDGEGPLTHAGVYAAEEVALIMKEKQICLQSLYTDQFQRL

Parental  QHLLKEKKRRYLHNRKVEHEALGNSLLTGPEGLLAKERENLKRLKCLRRYRQRYGVEALLHRQLKERRML
          QHL.KEKKR.YLHN.KVE.EALG.SL.TG.EGLLAKEREN.K.LKCLR...Q..G.EAL..RQL.E.RM.
Retrocopy QHLFKEKKRSYLHNQKVEQEALGSSLPTGSEGLLAKERENSKQLKCLR*CCQHNGAEALVQRQLRECRMM

Parental  ATDGAAQQAHTTRSSQRCLAFVDDVRCSNQSLPMTRHCLTHICQDTNQVLFKCCQGSEEVPCNK-PVPVS
          AT.GAA.QA.TT.SSQRCLAFV..V.CSNQ.L.M.RH.LTHICQDTNQVLFKCCQ.SEEVPCNK..VPVS
Retrocopy ATHGAAHQARTTHSSQRCLAFVENVHCSNQALLMSRHFLTHICQDTNQVLFKCCQ*SEEVPCNK>TVPVS

Parental  LSEDPCCPLHFQLPPQMYKPEQDLDVVGDGMPCPPSPLLFDPSLTLEDHSVTESAGDAGQMQAAGDGCRS
          LSE.PC..LHFQL..Q.YKPE.DL.V.GDGM..P.SPLLFDPSLTLEDHSVTE.A...GQMQ..G.GCRS
Retrocopy LSEVPCRLLHFQLSLQIYKPE*DLGVMGDGMS*PLSPLLFDPSLTLEDHSVTETARGPGQMQLVGAGCRS

Parental  QGARSVE
          QG.R..E
Retrocopy QGPRNIE

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	8.48 RPM
SRP007412_cerebellum	0.00 RPM	8.16 RPM
SRP007412_heart	0.00 RPM	12.95 RPM
SRP007412_kidney	0.00 RPM	8.39 RPM
SRP007412_liver	0.00 RPM	5.73 RPM
SRP007412_testis	0.00 RPM	6.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3134 was not detected

EST

No EST(s) were mapped for retro_mmus_3134 retrocopy.

TSS

No TSS is located nearby retro_mmus_3134 retrocopy 5' end.

Lab

retro_mmus_3134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3134 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005760	1 retrocopy	retro_cpor_1491,
Dipodomys ordii	ENSDORG00000001180	1 retrocopy	retro_dord_474,
Mus musculus	ENSMUSG00000022992	2 retrocopies	retro_mmus_2944, retro_mmus_3134 ,
Rattus norvegicus	ENSRNOG00000010904	3 retrocopies	retro_rnor_1071, retro_rnor_2831, retro_rnor_792,
Tupaia belangeri	ENSTBEG00000016536	1 retrocopy	retro_tbel_1374,