RetrogeneDB ID: retro_pabe_1358

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:40411573..40412207(+)
• Located in intron of: ENSPPYG00000007348

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIP13
• Ensembl ID: ENSPPYG00000015309
• Aliases: None
• Description: thyroid hormone receptor interactor 13 [Source:HGNC Symbol;Acc:12307]

Sequence

>retro_pabe_1358
TATGGTACTGTGTTTGGTGATTACACATGGACTGAGTTTGGTGAACCCTTTCTGACCAGGAACATGCGGGATTCTATTGT
TGACACAGAATTAAAAGTTAAAGACCCATAGCTCATTGATGAGTGCGTGCGCTATTGCACTTCACATCTTCCAGCAGAAT
GAAGATGGCCCTAGCAGTGAAAATTTGGAGGAAGAGACAGAAGATGTAATTGTGGCAAATCACTGGGTTCTGCCTGCTGT
CAAATTCCATGGGCTTTGGAACAGCCTAGTGTCTGATGTGGAAATCAAATCACACCTTGATTATGTGATTACAGTCTTAC
CATTTTCAGACAAGAATGTCAACAGCAGCCTCAGCACCTGGAACCAGGTGGTGCTGCTACAGGGTCCTCCAGGAACTGGA
AAAACATTCCTATGTAAAGCATTAGCCCACAAATTGACTATTAAACTTTCAAGCAGGTATTGGTATGGCCAATTAATTGA
AATAAATAGCCCTAACCTCTTTTCTAAACGGTTTTCTGAAAGTGACAAGCTGATAACTAAGACGTTCCAGAAGATTCAGG
ATTTGATTGATTATAAAGATGCTCTGGCATTTTCACTGATTGATGAGATAGAAAGTCTCACAGCCACCCATAAT

Alignment

ORF - retro_pabe_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HNIVFGDYTWTEFDEPFLTRNVQSVSIVDTEL-KVKDSQPIDLSACTVALHIFQLNEDGPSSENLEEETE
          ...VFGDYTWTEF.EPFLTRN....SIVDTEL.K.K.......SAC..ALHIFQ.NEDGPSSENLEEETE
Retrocopy YGTVFGDYTWTEFGEPFLTRNMRD-SIVDTEL>KLKTHSSL-MSACAIALHIFQQNEDGPSSENLEEETE

Parental  NIIAANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTS
          ..I.ANHWVLPA..FHGLW.SLV.DVE.KSHL.DYV.T.L.FSDKNVNS.L.TWN.VVLL.GPPGTGKT.
Retrocopy DVIVANHWVLPAVKFHGLWNSLVSDVEIKSHL-DYVITVLPFSDKNVNSSLSTWNQVVLLQGPPGTGKTF

Parental  LCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDEVESL
          LCKALA.KLTI.LSSRY.YGQLIEINS..LFSK.FSES.KL.TK.FQKIQDLID.KDAL.F.LIDE.ESL
Retrocopy LCKALAHKLTIKLSSRYWYGQLIEINSPNLFSKRFSESDKLITKTFQKIQDLIDYKDALAFSLIDEIESL

Parental  TAARN
          TA..N
Retrocopy TATHN

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	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.12 RPM
SRP007412_heart	0.06 RPM	0.03 RPM
SRP007412_kidney	0.03 RPM	0.03 RPM
SRP007412_liver	0.09 RPM	0.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1358 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1358 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1987

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007439	1 retrocopy	retro_chof_2003,
Callithrix jacchus	ENSCJAG00000003849	1 retrocopy	retro_cjac_1987,
Dasypus novemcinctus	ENSDNOG00000015202	1 retrocopy	retro_dnov_2464,
Oryctolagus cuniculus	ENSOCUG00000006144	1 retrocopy	retro_ocun_155,
Pongo abelii	ENSPPYG00000015309	1 retrocopy	retro_pabe_1358 ,