RetrogeneDB ID: retro_pabe_397

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:66024747..66025797(-)
• Located in intron of: ENSPPYG00000000420

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT2B
• Ensembl ID: ENSPPYG00000020545
• Aliases: TRMT2B, CXorf34
• Description: tRNA (uracil(54)-C(5))-methyltransferase homolog [Source:RefSeq peptide;Acc:NP_001124606]

Sequence

>retro_pabe_397
GCTCAAGGTGAAATTTTACAAAGACTAGAGTCTCACATCCAAATGCTCGATGGAGTCAAGTGACAACAGCTGCACCCAAA
TCTGAGGGGCTGTCTTGTCTTCTCCATCCTATAATACCATCTCCTGTCGTCAGTGGCTACAGAAATAAGTCCGCCTTCTC
TGTGAATCAGGGTCTGGATGGCAGTCCAAAGACTGTGGAATATGACCTGGGAACTTGAAGAGATGGGAACATCGTCTGTG
TACAGTCTAACCATCTGAAAAACATCCCTGAGAAACACAATCAGGTGGCACAGTACTATGAAGTAGTCCTTCCACAGTCT
CCAAAAGAGCCCTGCCTTCTTCGTGAAGGTGGATACTGGTGTGAGCTCACAGTCCGCACCAATAGCCTAAGGCACACAAT
GGCTGTCATCACATTCCATCCCCAGGAATTAAGTCCAGAGGAGCTCCATGTTCAGGAGACTGTAAAGGAATTTTTCATTA
AAGGTCCTGGAGCAGTGTGTGACTTGACTTCACCTGACTTCCAGGAAAGCAGGACCCGTTTCAGCCATCATCAGTCCACC
TACCAGCTCTTGTTTGGGGAACCTCATATCTTTAAAGATCTCCTGGGCTTGAAGGTCTGCATCTGTCCAGATGCCTTTTT
CCAGATTAACACTGCTGGTGCAGAGATGCTGTATTGAATTGTGGGGAAGCTGAGTGGAGTGAACTCTAACACCATCCTCC
TTGACATCTGCTGTGGAACCGGTGTGATCAGCCTCCCTTTGGCTCAGCTATATCGCAGGTCCTTGGGATTTCGATGGTGG
GGCAGGCAGTGGAGGATGCTAGGCAGACTGCAGCCTACAATGGCATCACCAGCTTTGAGTTTCATACTGGTCAAGCAGAG
ATTTTTCCAGGGCTGCTAAAGTCAAAGGAAGGTGGACAGTTAATTGTTGCTATGTGAACCCAGCCCATGCTGAACTGCAT
TACAAGGAAGTTCAAGCCATTTGAAACTTCAAGGCCCTCCGCATACTAGCTTTTGTTTCCTGCAGGCCCCGTGATGAAAC
CACAAGGAAT

Alignment

ORF - retro_pabe_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.58 %
• Parental protein coverage: 70.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AQKKILQRLESYIQMLNGVS-VTTAVPKSERLSCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGFY
          AQ..ILQRLES.IQML.GV..VTTA.PKSE.LSCLLHPIIPSPV..GYRNKS.FSVN.G.DG.PKTV...
Retrocopy AQGEILQRLESHIQMLDGVK<VTTAAPKSEGLSCLLHPIIPSPVVSGYRNKSAFSVNQGLDGSPKTVEYD

Parental  LGTWRDGNMVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTMAIIT
          LGT.RDGN.VCVQSNHLKNIPEKH.QVAQYYEV.L.QSP.EPCL...EGGYW.ELTVRTNS..HTMA.IT
Retrocopy LGT*RDGNIVCVQSNHLKNIPEKHNQVAQYYEVVLPQSPKEPCLL-REGGYWCELTVRTNSLRHTMAVIT

Parental  FHPQNLSQEELHVQKEIVKEFFIRGPGAACDLTSLYFQESTMTRCSHQQSPYQLLFGEPYIFEELLSLKI
          FHPQ.LS.EELHVQ.E.VKEFFI.GPGA.CDLTS..FQES..TR.SH.QS.YQLLFGEP.IF..LL.LK.
Retrocopy FHPQELSPEELHVQ-ETVKEFFIKGPGAVCDLTSPDFQES-RTRFSHHQSTYQLLFGEPHIFKDLLGLKV

Parental  RISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGLSLSQ-HTSRVLGIELVEQAVEDAR
          .I.PDAFFQINTAGAEMLY..VG.L.GVNS.TILLDICCGTGVI.L.L.Q...S.VLGI..V.QAVEDAR
Retrocopy CICPDAFFQINTAGAEMLY*IVGKLSGVNSNTILLDICCGTGVISLPLAQ<AISQVLGISMVGQAVEDAR

Parental  WTAAFNGITNSEFHTGRAEKILPGLLKSKEDGQSIVAV-VNPARAGLHYKVIQAIRNFRAIHTLVFVSCK
          .TAA.NGIT..EFHTG.AE.I.PGLLKSKE.GQ.IVA..VNPA.A.LHYK..QAI.NF.A...L.FVSC.
Retrocopy QTAAYNGITSFEFHTGQAE-IFPGLLKSKEGGQLIVAM<VNPAHAELHYKEVQAI*NFKALRILAFVSCR

Parental  LHGESTRN
          ...E.TRN
Retrocopy PRDETTRN

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	9.01 RPM
SRP007412_cerebellum	0.24 RPM	5.72 RPM
SRP007412_heart	0.06 RPM	10.96 RPM
SRP007412_kidney	0.00 RPM	18.99 RPM
SRP007412_liver	0.00 RPM	10.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_397 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_397 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_272
Pan troglodytes	retro_ptro_228
Gorilla gorilla	retro_ggor_319
Macaca mulatta	retro_mmul_567

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004570	1 retrocopy	retro_cjac_1676,
Homo sapiens	ENSG00000188917	1 retrocopy	retro_hsap_272,
Gorilla gorilla	ENSGGOG00000023759	1 retrocopy	retro_ggor_319,
Macropus eugenii	ENSMEUG00000006532	2 retrocopies	retro_meug_1325, retro_meug_74,
Macaca mulatta	ENSMMUG00000010394	1 retrocopy	retro_mmul_567,
Monodelphis domestica	ENSMODG00000025630	1 retrocopy	retro_mdom_77,
Nomascus leucogenys	ENSNLEG00000007522	1 retrocopy	retro_nleu_1485,
Pongo abelii	ENSPPYG00000020545	1 retrocopy	retro_pabe_397 ,
Pan troglodytes	ENSPTRG00000023413	1 retrocopy	retro_ptro_228,