RetrogeneDB ID: retro_pabe_2721

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:16402869..16404172(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSPPYG00000013702
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:HGNC Symbol;Acc:17341]

Sequence

>retro_pabe_2721
ATGCTGAGGTGCCTGTATCATTGGCACAGGCCAGTGCTGAACTGTAGGTGGAGTAGGCTGTGCCTTCTGAAGCGGTATCT
ATTTACAATGAAGTTGCAGTCTCCCGAATTCCAGTCACTTTTCACAGAAGGATTGAAGAGTCTGACAGAATTATTTGTCA
AAGAGAATCACGAATTAAGAATAGCAGGAGGAGCAGTGAGGGATTTATTAAATGGAGTAAAACCTCAGGATATAGATTTT
GCCACCACTGCTACCCCTACTTAAATGAAGGAGATGTTTCAGTCGGCTGGGATTCGGATGATAAACAACAGAGGAGAAAA
ACACGGAACAATTACTGCCAGGCTTCATGAAGAAAATTTTGAGATTACTACACTACGGATTGATGTCACCACTGATGGAA
GACATGCTGAGGTAGCATTTACAACTGACCGGCAGAAAGATGTGGAATGCAGAGATCTCACTATAAAATTGTATGTTTTT
AGGTTTTGATGGCACTTTATTTCACTACTTTAATGGTTATGAAGATTTAAAAAATAAGAAAGTTAGATTTGTTGGACATG
CTAAACAGAGAATACAAGAGGATTATCTTAGAATTTTAAGATACTTCAGGTTTTATGGGAGAATTGTAGACAAACCTGGT
GACCATGATCCTGAGACTTTGGAAGCAATTGCAGAAAATGCAAAAGGCTTGGCTGGAATATCAGGAGAAAGGATTTGGGT
GGAACTGAAAAAAATTCTTGTTGGTAACCACGTAAATCATTTGATTCACCTTATCTATGATCTTGATGTGGCTTCTTATA
TAGGTTTACCTGCTAATGCAAGTTTAGAAGAATTTGACAAAGTCAGTAAAAATGTTGAAGGTTTTTCACCAAAGCCAATG
ACTCTTTTGGCCTCATTATTCAAAGTACAAGATGATGTCACAAAATTGGATTTGAGGTTGAAGATCTCAAAAGAAGAGAA
AAACCTTGGCTTATTTATAGTTAAAAATAAGAAAGATTTAATTAAAGCAACAGATAGTTCAGACCCATTGAAACCCTATC
AAGACTTCATTATAGATTCTAGGGAACCTGATGCACCTACTCGTGTATGTGAACTACTCAAGTACCAAGGAGAGCACTGT
CTCCTAAAGGAAATGCAGCAGTGGTCCATTCCTCCATTTCCTGTAAGTGGCCATGACATCAGAAAAGTGGGCATTTCTTC
AGGAAAAGAAATTGGGGCTCTATTACAACAGTTGCGAGAACAGTGGAAAAAAAGTGGTTACCAAATGGAAAAAGATGAAC
TTCTGAATTACATAAAGAAGACC

Alignment

ORF - retro_pabe_2721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRCLYHWHRPVLNCRWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLL
          MLRCLYHWHRPVLNCRWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLL
Retrocopy MLRCLYHWHRPVLNCRWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLL

Parental  NGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEF
          NGVKPQDIDFATTATPT.MKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEV.F
Retrocopy NGVKPQDIDFATTATPT*MKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVAF

Parental  TTDWQKDAERRDLTI-NSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIV
          TTD.QKD.E.RDLTI.N.MFLGFDGTLF.YFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIV
Retrocopy TTDRQKDVECRDLTI>NCMFLGFDGTLFHYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIV

Parental  DKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFD
          DKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVA.YIGLPANASLEEFD
Retrocopy DKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVASYIGLPANASLEEFD

Parental  KVSKNVEGFSPKPMTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNKKDLIKATDSSEPLKPYQDF
          KVSKNVEGFSPKPMTLLASLFKVQDDVTKLDLRLKI.KEEKNLGLFIVKNKKDLIKATDSS.PLKPYQDF
Retrocopy KVSKNVEGFSPKPMTLLASLFKVQDDVTKLDLRLKISKEEKNLGLFIVKNKKDLIKATDSSDPLKPYQDF

Parental  IIDSREPDAPTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSG
          IIDSREPDAPTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSG
Retrocopy IIDSREPDAPTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSG

Parental  YQMEKDELLSYIKKT
          YQMEKDELL.YIKKT
Retrocopy YQMEKDELLNYIKKT

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	0.22 RPM	4.92 RPM
SRP007412_cerebellum	0.00 RPM	5.11 RPM
SRP007412_heart	0.03 RPM	2.20 RPM
SRP007412_kidney	0.00 RPM	5.67 RPM
SRP007412_liver	0.06 RPM	2.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2721 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721 , retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,