RetrogeneDB ID: retro_pabe_3135

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:41298405..41299307(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSPPYG00000017146
• Aliases: None
• Description: t-complex 1 [Source:HGNC Symbol;Acc:11655]

Sequence

>retro_pabe_3135
AGTATGCTTATTAGTGGCTATGCACTCAACTGTGTGGTGGGATCCCAGGGCATACCCAAGAGAATTGTAAATGCAAAAAT
TGCTTGCCTTGACTTTGGCCTGCAAAAAACAAAAATGAAGCTTGGTATACAGGTGGTCATTACAGACCCTGAAAAACTGG
ACCAAATTAGACAGAGAGAATCAAATATTACCAAGGAGAGAATTCAGAAGATCCTGGTAACTGGTGCCAGCATTATTCTA
ACCACTGGTGGAATTGATGATATGTGTCTGAAGTATTTTGTGGAGGCTGGTGCTATGGCAGTTAGAAGAGTTTTTAAAAG
GGACCTTAAATGCATTCCGAAAGCTTCTGGAGCAACTATTCTGTCAACTCTGGCCAATTTGGAAGGTGAATAAACTTTTG
AAGCTGCAATGTTGGGGCAGGCAGAAGAAGTGGTATAGCAGAGAATTTGTGATGATGAGCTGATCTTAATCAAAAACACT
AAGGCTCGTACATCTGCATCGATTATCTTACGTGGGACAAATGATTACATGTGGGATGAGATGGAGCATTCTTTACATGA
TGCTTTTTGTGTAGTGAAGATAGTTTTGGTGTCAAAATCTGTGGTTCCAGGTGGGGGTGCTGTAGAAGTAGCCCTTTCTA
TATACCTTGAAAACCATGCAACCAGCATGGGGTCTCGGGAACAGACTGCTATTGCAGAGTTTGCAAGATCACTTCTTGTA
TTCCTAACACACTGGCAGTTAATGCTGCCCAGGAATCCACAGATCTGGTTGCAAAGTTAAGAGCTTTTCATAATGAGGCT
CAGGTTAACCCAGAACGTAAAAATCTAAAATGGATTGGTCTTGATTTGAGCGATGGTAAACCTCGAGACAACAAACAAGC
AGGGGTGATTGAACCAACCATA

Alignment

ORF - retro_pabe_3135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.06 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQK
          SMLISGYALNCVVGSQG.PKRIVNAKIACLDF.LQKTKMKLG.QVVITDPEKLDQIRQRES.ITKERIQK
Retrocopy SMLISGYALNCVVGSQGIPKRIVNAKIACLDFGLQKTKMKLGIQVVITDPEKLDQIRQRESNITKERIQK

Parental  ILTTGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQ
          IL.TGA..ILTTGGIDDMCLKYFVEAGAMAVRRV.KRDLK.I.KASGATILSTLANLEGE.TFEAAMLGQ
Retrocopy ILVTGASIILTTGGIDDMCLKYFVEAGAMAVRRVFKRDLKCIPKASGATILSTLANLEGE*TFEAAMLGQ

Parental  AEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEA
          AEEVV..RICDDELILIKNTKARTSASIILRG.ND.M.DEME.SLHDA.CVVK.VL.SKSVVPGGGAVE.
Retrocopy AEEVV*QRICDDELILIKNTKARTSASIILRGTNDYMWDEMEHSLHDAFCVVKIVLVSKSVVPGGGAVEV

Parental  ALSIYLENYATSMGSREQLAIAEFARSLLV-IPNTLAVNAAQDSTDLVAKLRAFHNEAQVNPERKNLKWI
          ALSIYLEN.ATSMGSREQ.AIAEFARSLLV.IPNTLAVNAAQ.STDLVAKLRAFHNEAQVNPERKNLKWI
Retrocopy ALSIYLENHATSMGSREQTAIAEFARSLLV<IPNTLAVNAAQESTDLVAKLRAFHNEAQVNPERKNLKWI

Parental  GLDLSNGKPRDNKQAGVFEPTI
          GLDLS.GKPRDNKQAGV.EPTI
Retrocopy GLDLSDGKPRDNKQAGVIEPTI

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	39.92 RPM
SRP007412_cerebellum	0.00 RPM	37.45 RPM
SRP007412_heart	0.00 RPM	19.81 RPM
SRP007412_kidney	0.07 RPM	20.15 RPM
SRP007412_liver	0.03 RPM	15.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3135 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135 ,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,