RetrogeneDB ID: retro_ptro_228

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:163175991..163177045(+)
• Located in intron of: ENSPTRG00000001772

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT2B
• Ensembl ID: ENSPTRG00000023413
• Aliases: None
• Description: None

Sequence

>retro_ptro_228
GCTCAAGGTGAAATTTTACAAAGACTAGAGTCTCACATCCAAATGCTCGATGGAGTCAATGTGACAACAGCTGCACCCAA
ATCTGAGGGGCTGTATTGTCTTCTCCATCCTATAATACCATCTCCTGTCATCAGTGGCTACAGAAATAAGTCCACCTTCT
CTGTGAATCAGGGTCCAGATGGCAATCCAAAGACTGTGGAATATGACCTGGGAACTTGAAGAGACGGGAACATCGTCTGT
GTACAGTCTAACCGTCTGAAAAACATCCTTGAGAAACACAGTCAGGTGGCACAGTACTATGAAGTATTCCTTCCACAGTC
TCCAACAGAGCCCTGCCTTCTTCATGAAGGTGGTTACTGGTGTGAGCTCACAGTCCACACCAATAGCCTAAGGCACACAA
TGGCTGTCATCACATTCCATCCCCAGGAATTAAGTCCAGAGGAGCTCCATGTTCAGAAGGAGACTGTAAAGGAATTTTTC
ATTAAAGGTCCTGGAGCAGTCTGTGACTTGACTTCACCTGACTTCCAGGAAAGCAGGACCTGTTTCAGCCATCATCAGTC
CACCTACCAGCTCTTGTTTGGGGAACCTTATATCTTTAAAGATCTCCTGGGCTTGAAGGTCTGCATCTCTCCAGATGCCT
TTTTCCAGATTAACACTGCTGGTGCAGAGATGCTGTATTGGATTGTAGGGAAGCTGAGTGCAGTGAACTCTAACACCATC
CTCCTTGACATCTGCTGTGGAACTGGTGTGATCAGCCTCCCTCTGGATCAGCTACATCGCAGGTCCTTGGGATTTCATTG
GTGGGGCAGGCAGTGGAGGATGCTAGGCAGACTGCAGCCTACAATGGCATCACCAGCTTTGAGTTTCATACTGGTCAAGC
AGAGATTTTTCCAGGGCTGCTAAAGTCAAAGGAATATGGACAGTTAATTGTTGCTATGTGAACCCAGCCCATGCTGAACT
GCATTACAAGGAAGTTCAAGCCATTTGAAACTTCAAGGCCCTCAGCATACTAGCTTTTGTTTCCTGCAAGCCCCGTGATG
AAACCACAAGGAAT

Alignment

ORF - retro_ptro_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.75 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQKKILQRLESYIQMLNGVSVTTAVPKSERLSCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGFYL
          AQ..ILQRLES.IQML.GV.VTTA.PKSE.L.CLLHPIIPSPVI.GYRNKSTFSVN.GPDGNPKTV...L
Retrocopy AQGEILQRLESHIQMLDGVNVTTAAPKSEGLYCLLHPIIPSPVISGYRNKSTFSVNQGPDGNPKTVEYDL

Parental  GTWRDGNVVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTMAIITF
          GT.RDGN.VCVQSN.LKNI.EKHSQVAQYYEVFL.QSP.EPCL..HEGGYW.ELTV.TNS..HTMA.ITF
Retrocopy GT*RDGNIVCVQSNRLKNILEKHSQVAQYYEVFLPQSPTEPCLL-HEGGYWCELTVHTNSLRHTMAVITF

Parental  HPQKLSQEELHVQKEIVKEFFIRGPGAACGLTSLYFQESTMTRCSHQQSPYQLLFGEPYIFEELLSLKIR
          HPQ.LS.EELHVQKE.VKEFFI.GPGA.C.LTS..FQES..T..SH.QS.YQLLFGEPYIF..LL.LK..
Retrocopy HPQELSPEELHVQKETVKEFFIKGPGAVCDLTSPDFQES-RTCFSHHQSTYQLLFGEPYIFKDLLGLKVC

Parental  ISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGLSLAQ-HTSRVLGIELVEQAVEDARW
          ISPDAFFQINTAGAEMLY..VG.L..VNS.TILLDICCGTGVI.L.L.Q..TS.VLGI.LV.QAVEDAR.
Retrocopy ISPDAFFQINTAGAEMLYWIVGKLSAVNSNTILLDICCGTGVISLPLDQ<ATSQVLGISLVGQAVEDARQ

Parental  TAAFNGITNSEFHTGQAEKILPGLLKSKEDGQSIVAV-VNPARAGLHYKVIQAIRNFRAIHTLVFVSCKL
          TAA.NGIT..EFHTGQAE.I.PGLLKSKE.GQ.IVA..VNPA.A.LHYK..QAI.NF.A...L.FVSCK.
Retrocopy TAAYNGITSFEFHTGQAE-IFPGLLKSKEYGQLIVAM<VNPAHAELHYKEVQAI*NFKALSILAFVSCKP

Parental  HGESTRN
          ..E.TRN
Retrocopy RDETTRN

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	8.99 RPM
SRP007412_cerebellum	0.07 RPM	8.64 RPM
SRP007412_heart	0.12 RPM	14.40 RPM
SRP007412_kidney	0.03 RPM	18.20 RPM
SRP007412_liver	0.03 RPM	11.42 RPM
SRP007412_testis	0.21 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_228 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_228 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_272
Gorilla gorilla	retro_ggor_319
Pongo abelii	retro_pabe_397
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 ,