RetrogeneDB ID: retro_mmul_1925

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:167582076..167583047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN2
• Ensembl ID: ENSMMUG00000007195
• Aliases: None
• Description: None

Sequence

>retro_mmul_1925
GAGAGTACAGTACGCAGAATCCTCAAGGATTACATGAAACCGCTTGAGCGTCCCTCTGGGAAAAGGAATGAACAGGCTCA
AATGCATGATAGGTTTAACTCTGGAATGGTTTCCAACATGGAAGGTACAGCGGTAGGAGAGAGACCTTCTGTGATAAACG
GGGACTCTGGAAAGTCAGGTGTTATGGGTGATCCCAGTGAGTCATCAGGCTGCCTGCAGGAGGGCTCTGGCCACGACCCA
CCAACAGACGGCTTTGAGGAAAGCGTGGGAGAGGACGCTTCACCTCTGCCCCAAGTATGTTCCTGCAGACACGATGCTCT
CGTCCTCCCGTGTGGCCCTTACCGTGAGGACAGCAGCCAGCATTTTGGTCTCCTGCATGTTGGGGACAGAGGGCCTGACC
ACGAGTACATGCTGGTGCAGGAAGCCGAGTGTGCGTGAGCGAGAGGAAGGATGCCCCAAATGAGGAACTGGTGCAAAGAG
ACGAATCTGCAGAAGAAATCCATATAGGATCTTTGAGTATTTGCGACTCAGCCTAGAGGAGGCCTTCTTCCAGGTCTGTG
CTCTGGAATGTTTAAGTATTTGCTATGACAAGGAGCCTTTAACGATAGTGAAGCTCTGGAAAGCTTTCACTGTAGTTCAG
CCCACGTTCAGGACCACCTACATGGCCTACCATTACTTCCTAAGCAAGAGCTGGTGCCCAAAGTGGTGCTCAAGTACGGG
ATGGATTTACTGCTATGTTGGAAAGGCCCTCCGCTTACCATGCAAGCTATTCTGTCATTATTGAGCTAGTTGATGAGCAT
TTTGAAGGCTCTCTCTGCAGGCCTTTCAGTTAGATGTCCCTGACTGCCTTGAGCAGAGTTTCCATTAATGTCTCCAAGGA
ACTCATACTGTGCTCTTTCATTAAATCCTCTACCATGACTGACAAGGAAATGGAGTCACCAGAGTATATGAAAAGAATTA
GAGTTCACGAG

Alignment

ORF - retro_mmul_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 70.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ESTVCRILKDYTKPLEHPPVKRNEEAQVYDELNSGMVSNMEGTARGERPSVVNGDSGKSGGMGDPSEPLG
          ESTV.RILKDY.KPLE.P..KRNE.AQ..D..NSGMVSNMEGTA.GERPSV.NGDSGKSG.MGDPSE..G
Retrocopy ESTVRRILKDYMKPLERPSGKRNEQAQMHDRFNSGMVSNMEGTAVGERPSVINGDSGKSGVMGDPSESSG

Parental  SLQEGSGCNPTTDGFEKSVRKDAAPLPQVCCCKQDALILQCGPHHEDGSQHVGLLHAGDRGPDHEYVLVE
          .LQEGSG..P.TDGFE.SV..DA.PLPQVC.C..DAL.L.CGP..ED.SQH.GLLH.GDRGPDHEY.LV.
Retrocopy CLQEGSGHDPPTDGFEESVGEDASPLPQVCSCRHDALVLPCGPYREDSSQHFGLLHVGDRGPDHEYMLVQ

Parental  EVECA-MSEREDAPNEELVQRN-RLICRRNPYRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLW
          E.ECA..SER.DAPNEELVQR..R...R.NPYRIFEYL.LSLEEAFF.V.AL.CLSI.Y.KEPLTIVKLW
Retrocopy EAECA<VSERKDAPNEELVQRD<RICRR-NPYRIFEYLRLSLEEAFFQVCALECLSICYDKEPLTIVKLW

Parental  KAFTVVQPTFRTTYMAYHYFRSKGW-VPKVGLKYGTDLLLYRKGPPF-YHASYSVIIELVDDHFEGCLRR
          KAFTVVQPTFRTTYMAYHYF.SK.W.VPKV.LKYG.DLLL..KGPP..YHASYSVIIELVD.HFEG.L.R
Retrocopy KAFTVVQPTFRTTYMAYHYFLSKSW<VPKVVLKYGMDLLLCWKGPPL<YHASYSVIIELVDEHFEGSLCR

Parental  PFSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQE
          PFS..SL.ALSRVS.NVSKEL.LC..IK.STMTDKEMESPE.MKRI.V.E
Retrocopy PFS*MSLTALSRVSINVSKELILCSFIKSSTMTDKEMESPEYMKRIRVHE

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	13.89 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.25 RPM
SRP007412_cerebellum	0.00 RPM	17.37 RPM
SRP007412_heart	0.00 RPM	7.42 RPM
SRP007412_kidney	0.00 RPM	14.44 RPM
SRP007412_liver	0.00 RPM	5.86 RPM
SRP007412_testis	0.00 RPM	5.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1925 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1925 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3011
Pan troglodytes	retro_ptro_2035
Gorilla gorilla	retro_ggor_2085
Pongo abelii	retro_pabe_2495

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154743	1 retrocopy	retro_hsap_3011,
Gorilla gorilla	ENSGGOG00000012488	2 retrocopies	retro_ggor_1826, retro_ggor_2085,
Microcebus murinus	ENSMICG00000016672	1 retrocopy	retro_mmur_883,
Macaca mulatta	ENSMMUG00000007195	1 retrocopy	retro_mmul_1925 ,
Pongo abelii	ENSPPYG00000013647	1 retrocopy	retro_pabe_2495,
Pan troglodytes	ENSPTRG00000014633	1 retrocopy	retro_ptro_2035,