RetrogeneDB ID: retro_pabe_3709

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:145469960..145471598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT1
• Ensembl ID: ENSPPYG00000009622
• Aliases: None
• Description: tRNA methyltransferase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25980]

Sequence

>retro_pabe_3709
CCCAGCGCCAACGAGGTCTTTTATAACCTTGTGCAGGAATTCAATCGGGACACGACATGTGCTGTGATCATCCAGTTTGC
TCGCATTCAGCTTGGGGCCAAAGGAATCCAGATCAAGGTGCCAGGAGAGAAGGATACACAAAAGGCTGTCGTGGACTTGT
GAAAGCAAGAGGAGGAAAAGGTTGAACCGAAAGAGAGTGAAAACCTGGCCTCAGGAGACCAACCTCGCACAGCGACCGTG
TGGGAGATCTGCGAGGAAGGCCTGCAAGTGCTGGAAGGCCTGGCAGCTTCAGGCCTACGTTCCATTCGATTTGCCCTAGA
GGTGCCTGGGCTCAGATCTGTGGTTGCAAACGATGCCTCTGTCCGGGCTGTGGATCTCATACGCTGGAATGTGCAGCTCA
ATGACGTGGCCCACCTGGTACAGCCCAGCCAAGTAGATGCCTGGATGCTGATGTACCAGCACCAGAGGGTGTCGGAGAGG
TTCGACGTCATCCATCTGGACCCCTATGGCAGTCCTGCGCCCTTCCTGGATGCAGCTGTGCAGGCTGTGAGTGAAGGAGA
GTTGCTGTGCGTGACCTGCACGGACATGGCGGTGCTGGCGCAGAACAGCGGGGAGATGTGTTACAGCGAGTTCGGTGCCA
TGGCCCTCAAGAGCCGGGCCTGCCACGAGATGGCCCTGAGAATCGTCCTGCACAGCCTGGACCTCCGCGCCAACTGTTAC
CAGCGCTTCCTGGTGCCGCTGCTTAGCATCAGCGCCGACTTCCACGTGCGTGTTTTTGTACGTGTCTTCACCGGCCAGCC
CAAGGTTAAGGCCTCAGCCAGCAAGCAGGCGCTGGTGTTCCAGTGTGTGGGCTGCCGGGCCTTCCATCTTCAGCGCCTCG
GCAAAGCGTCAGGAGTCCCCCGCGGCCGGGTCAAGTTCTCTGCAGCCTGTGTTCCCCCCGTGACCCCGAGTGTGAACACT
GTGGGCAGCGACACCAGCCTGGTTGCTCCATGTGGGCAGAGGCCATCCATGACTTGGATTTCGTGAGCTGTGTCCTAGAG
GCTGTGAGCGCTAACCCCGGCCACTTCCACACCTCGGAGCGGATGCCAGAGGGTCCTGAGAGTCATGACTGAGGAGCTCC
CGGAGGTGCCTCTGTACTACACCCTGGACCAGCTGAGCAGCACCATCCTCTGCAACACGCCCAGCCTCCTGTTGTTGCGG
TCGGCCCTCCTCCACGCTCACTTCCGGGTTTCGCTCTCCCACGCCTGTAAGAACGCTGTGAAGACGTATGCCCCGCCTCT
GCCCTCTGAAACATCACGCGCTGCTGGAAGAAGGAATGTCCGGTGAAACAGGAGCGACTCTCAAGAGACCAGCCCAGCGT
CCGGCATTCTCAGTGTGGAGCCCAGGCTGCAGGGCAACTTCACCATCCGGGAAAATGCCAACCCCAGCTCCCGCCAGCGA
CGACTCCAGCGCTTCCGGGCCAACCCGGAAGCAAACTGGGGCCCGAGGCCTCATGCCTGGCCAGGGAGCAAGGCTGCCGG
CGAAGCTATGGAGGAGAGACGCAGGCTGCTTCCTAAGGAGCGGAAGGAGCCGCCTGAGGACAGGGCCCAGCGAGCTGCCC
TGCTCAAGACATTTCCTTGCAAAAGGGTTAAGGAGGGG

Alignment

ORF - retro_pabe_3709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 82.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PSANEVFYNPVQEFNRDLTCAVITEFARIQLGAKGIQIKVPGEKDTQKVVVDLSEQEEEKVELKESENLA
          PSANEVFYN.VQEFNRD.TCAVI..FARIQLGAKGIQIKVPGEKDTQK.VVDL..QEEEKVE.KESENLA
Retrocopy PSANEVFYNLVQEFNRDTTCAVIIQFARIQLGAKGIQIKVPGEKDTQKAVVDL*KQEEEKVEPKESENLA

Parental  SGDQPRTAAVGEICEEGLHVLEGLAASGLRSIRFALEVPGLRSVVANDASARAVDLIRQNVQLNDVAHLV
          SGDQPRTA.V.EICEEGL.VLEGLAASGLRSIRFALEVPGLRSVVANDAS.RAVDLIR.NVQLNDVAHLV
Retrocopy SGDQPRTATVWEICEEGLQVLEGLAASGLRSIRFALEVPGLRSVVANDASVRAVDLIRWNVQLNDVAHLV

Parental  QPSQADARMLMYQHQRVSERFDVIDLDPYGSPATFLDAAVQAVSEGGLLCVTCTDMAVLAGNSGETCYSK
          QPSQ.DA.MLMYQHQRVSERFDVI.LDPYGSPA.FLDAAVQAVSEG.LLCVTCTDMAVLA.NSGE.CYS.
Retrocopy QPSQVDAWMLMYQHQRVSERFDVIHLDPYGSPAPFLDAAVQAVSEGELLCVTCTDMAVLAQNSGEMCYSE

Parental  YGAMALKSRACHEMALRIVLHSLDLRANCYQRFVVPLLSISADFYVRVFVRVFTGQAKVKASASKQALVF
          .GAMALKSRACHEMALRIVLHSLDLRANCYQRF.VPLLSISADF.VRVFVRVFTGQ.KVKASASKQALVF
Retrocopy FGAMALKSRACHEMALRIVLHSLDLRANCYQRFLVPLLSISADFHVRVFVRVFTGQPKVKASASKQALVF

Parental  QCVGCGAFHLQRLGKASGVPSGRVKFSAACGPPVT-PECEHCGQRHQLGGPVWAEPIHDLDFVGRVLEAV
          QCVGC.AFHLQRLGKASGVP.GRVKFSAAC.PPVT.PECEHCGQRHQ.G...WAE.IHDLDFV..VLEAV
Retrocopy QCVGCRAFHLQRLGKASGVPRGRVKFSAACVPPVT<PECEHCGQRHQPGCSMWAEAIHDLDFVSCVLEAV

Parental  SANPGRFHTSERI-RGVLSVITEELPDVPLYYTLDQLSSTIHCNTPSLLQLRSALLHADFRVSLSHACKN
          SANPG.FHTSER....VL.V.TEELP.VPLYYTLDQLSSTI.CNTPSLL.LRSALLHA.FRVSLSHACKN
Retrocopy SANPGHFHTSERM>QRVLRVMTEELPEVPLYYTLDQLSSTILCNTPSLLLLRSALLHAHFRVSLSHACKN

Parental  AVKTDA-PASALWDIMRCWEKECPVKRERLS-ETSPAFRILSVDPRLQANFTIREDANPSSRQRGLKRFQ
          AVKT.A.PASAL..I.RCW.KECPVK.ERLS.ETSPA..ILSV.PRLQ.NFTIRE.ANPSSRQR.L.RF.
Retrocopy AVKTYA<PASAL*NITRCWKKECPVKQERLS>ETSPASGILSVEPRLQGNFTIRENANPSSRQRRLQRFR

Parental  ANPEANWGPRPRARPGGKAADEAMEGRRRLLQNKRKEPPEDVAQRAARLKTFPCKRFKEG
          ANPEANWGPRP.A.PG.KAA.EAME.RRRLL...RKEPPED.AQRAA.LKTFPCKR.KEG
Retrocopy ANPEANWGPRPHAWPGSKAAGEAMEERRRLLPKERKEPPEDRAQRAALLKTFPCKRVKEG

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	22.67 RPM
SRP007412_cerebellum	0.00 RPM	12.28 RPM
SRP007412_heart	0.00 RPM	4.49 RPM
SRP007412_kidney	0.00 RPM	20.42 RPM
SRP007412_liver	0.03 RPM	12.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3709 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000104907	1 retrocopy	retro_hsap_4766,
Oryctolagus cuniculus	ENSOCUG00000021934	1 retrocopy	retro_ocun_1629,
Pongo abelii	ENSPPYG00000009622	1 retrocopy	retro_pabe_3709 ,
Pan troglodytes	ENSPTRG00000010557	1 retrocopy	retro_ptro_3173,