RetrogeneDB ID: retro_pabe_2495

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:182637163..182638550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN2
• Ensembl ID: ENSPPYG00000013647
• Aliases: None
• Description: tRNA splicing endonuclease 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28422]

Sequence

>retro_pabe_2495
ATGGCAGAAGCAGTTTTCCATGCCCCAAACAGGAAAGGAAGAATGTATGAGACTTATGAGTCTCCATTGCCAATCCTTTC
TGGTCAGGACCGTGGTCCTCAGAAAGCAAGATATTCTATGCTGAAATGATTAACAACAATGTGATTGTGAGGAATGCAGA
GGACATTGAGCAGCTCTATGGGGAAGGTTCTTTTGGAAAAGGTATTCTTTCAAGAAACTGTCCAGCGATCACAGTTTCAG
ATCCTAAATTGGTTGCGAAATGGAAAGATATGAAGACAAACATGCTTATCATCACATCAAAGAAGTATCAACGTAGTGTT
GAGTGGGTGGCAGAGCTGATGCGTAGACAGGGACAGAATGAGAATACAGTGCGCAGAATCCTCAAGGATTACATGAATCC
GCTTGAGCATCGCCCTGTGAAAAGGAATGAACAGGCTCAAATGCATGATGAGCTTAACTCTGGAATGGTTTCCAACGTGG
AAGGCACAGCGGTAGGAGAGAGATCTTCTGTGATAAACGGGGACTCTGGAAAGTCAGGTGTTATGGGTGATCCCAGTGAG
CCATTAGGCTGCCTGCAGGAGGGCTCTGGGAGCGACCCACCAACAGAAGGCTTTGAGGAAAGGGTGGGAGAGGACGCTTC
ACCTCCGCCCCAAGCATGTTGCTGCAAACACGATGCTCTTGTCCTCCCGTCTGGCCCTCACCGGGAGGACAGCAGCCAGC
ATTTTGGTCTCCTGCATGCTGGGGACAGAGGGCCTGACCAGTACGTGCTGGTGCAGGAAGCCGAGTGTGCAGTGAGCGAG
AGGAAGGATGCCTCAAATGAGGAATTGGTGCAAAGAAAGAGACTAATCTGCAGAAGAAATCCATATAGGATCTCTGAGTA
TTTGCAGCTCAGCCTAGAAGAGGCCTTTTTCCTGGTCTGTGCTCTGGAATGTTTAAGTATTTGCTACGAGAAGGAGCCTT
TAACGATAGTGAAGCTCTGGAAAGCTTTCACTGTAGTTCAGCCCACGTTTAGGACCACCTACATGGCCTACCATTACTTC
CCAAGCAAGGGCTAGTGCCCAGAGTGGGGCTCAAGTACGGGACAGATTTGCTGCTATGTTGGAAAGGCCCTCCGTTTTAC
CATGCAAGCTATTCTGTCGTTATTGAGCTAGTTGATGAGCAGTTTGAAGGCTGTCTCTGCAGGCCTTTCAGTTGGATGTC
CCTGGCTGCCTTGAGCAGAGTTTCCGTTAATGTCTCCAAGGAACTCATGCTGTGCTGTTTCATTAAACCCTCTACTATGA
CTGACAAGGAAATGGAGTCACCAGAATGTATGAAAAAAATTAGAGTTCAGGAGGTGATTCTGAGTTGATGGGTGTCTTCA
CGAGAGAGGAGTGACCAAGACGAACTT

Alignment

ORF - retro_pabe_2495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEAVFHAPKRKRRVYETYESPLPI-PFGQDHGP-QKEFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGK
          MAEAVFHAP.RK.R.YETYESPLPI.PF....GP...E.KIF.AEMINNNVIVRNAEDIEQLYG.G.FGK
Retrocopy MAEAVFHAPNRKGRMYETYESPLPI<PFWS--GPWSSESKIFYAEMINNNVIVRNAEDIEQLYGEGSFGK

Parental  GILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQRSVERAAELMCRQGQDESTVRRILKDYTKPLEH
          GILSR..P..T.SDPKLVAKWKDMKTNM.IITSK.YQRSVE..AELM.RQGQ.E.TVRRILKDY..PLEH
Retrocopy GILSRNCPAITVSDPKLVAKWKDMKTNMLIITSKKYQRSVEWVAELMRRQGQNENTVRRILKDYMNPLEH

Parental  PPVKRNEEAQVHDELNSGMVSNMEGTAGGVRPSVVNGDSGKSGGMGDPSEPFGCLQEGSGCDPTTDGFEK
          .PVKRNE.AQ.HDELNSGMVSN.EGTA.G.R.SV.NGDSGKSG.MGDPSEP.GCLQEGSG.DP.T.GFE.
Retrocopy RPVKRNEQAQMHDELNSGMVSNVEGTAVGERSSVINGDSGKSGVMGDPSEPLGCLQEGSGSDPPTEGFEE

Parental  SMGEDASLLPQVCCCKQDALILQCGPHHEDSSQHVGLLHAGDRGPDHEYVLVEEAQCAVSEREHVPNEEL
          ..GEDAS..PQ.CCCK.DAL.L..GPH.EDSSQH.GLLHAGDRGPD..YVLV.EA.CAVSER....NEEL
Retrocopy RVGEDASPPPQACCCKHDALVLPSGPHREDSSQHFGLLHAGDRGPD-QYVLVQEAECAVSERKDASNEEL

Parental  VQRNRLICRRNPYRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY
          VQR.RLICRRNPYRI.EYLQLSLEEAFFLV.AL.CLSI.YEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY
Retrocopy VQRKRLICRRNPYRISEYLQLSLEEAFFLVCALECLSICYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY

Parental  FRSK-GWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDHFEGSLRRPFSWKSLAALSRVSINVSKE
          F.SK.G.VP.VGLKYGTDLLL..KGPPFYHASYSV.IELVD..FEG.L.RPFSW.SLAALSRVS.NVSKE
Retrocopy FPSK<GLVPRVGLKYGTDLLLCWKGPPFYHASYSVVIELVDEQFEGCLCRPFSWMSLAALSRVSVNVSKE

Parental  LMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL
          LMLC..IKPSTMTDKEMESPECMK.I.VQEVILS.WVSSRERSDQD.L
Retrocopy LMLCCFIKPSTMTDKEMESPECMKKIRVQEVILS*WVSSRERSDQDEL

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_prefrontal_cortex	0.00 RPM	8.40 RPM
SRP007412_cerebellum	0.00 RPM	13.13 RPM
SRP007412_heart	0.00 RPM	4.82 RPM
SRP007412_kidney	0.00 RPM	6.23 RPM
SRP007412_liver	0.00 RPM	3.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2495 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2495 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
Macaca mulatta	retro_mmul_1925

---

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,