RetrogeneDB ID: retro_pabe_3478

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:56532022..56532433(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019230
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SELT
• Ensembl ID: ENSPPYG00000029483
• Aliases: None
• Description: selenoprotein T precursor [Source:RefSeq peptide;Acc:NP_001186922]

Sequence

>retro_pabe_3478
ATGCAGGTTATTAGCCAGTAGTACCCAGACATCCATATTGAAGGAGAGAATTACCTCCCTCAACCAATGTATAGACACAT
AGCATCTTTCCTGTCAGTCTTCAAACTAGTATTAATAGGCTTAATAATTGTTGGCAAGGATCGTTTTGCTTTCTTTGGCA
TGCAAGCTCCTAATATCTGGCAGTGGGGCCAAGAAAATAAGGTCTATTCGTGTATGATGGTTTTCTTCTTGAGCAACATG
ATTGAGAACCAGTGTATGTCAACAGGTGCATTTGAGACAACTTTAAATAATGCACCTGTGTGGTCTAAGCTGGAATCTGG
TCACCTTCCATCCATGCAACAACTTGTTCAAATTCTTGACAATGAAATGAAGCTCAATGTGCATATGGATTCAGTCTCAC
ACCATCGATCA

Alignment

ORF - retro_pabe_3478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYA
          M.VISQ.YPDI.IEGENYLPQP.YRHIASFLSVFKLVLIGLIIVGKD.FAFFGMQAP.IWQWGQENKVY.
Retrocopy MQVISQ*YPDIHIEGENYLPQPMYRHIASFLSVFKLVLIGLIIVGKDRFAFFGMQAPNIWQWGQENKVYS

Parental  CMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS
          CMMVFFLSNMIENQCMSTGAFE.TLN..PVWSKLESGHLPSMQQLVQILDNEMKLNVHMDS..HHRS
Retrocopy CMMVFFLSNMIENQCMSTGAFETTLNNAPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSVSHHRS

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	1.33 RPM	30.58 RPM
SRP007412_cerebellum	1.70 RPM	52.77 RPM
SRP007412_heart	0.39 RPM	18.72 RPM
SRP007412_kidney	0.33 RPM	27.21 RPM
SRP007412_liver	0.18 RPM	19.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3478 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3478 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4126
Pan troglodytes	retro_ptro_2804

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002576	1 retrocopy	retro_cpor_459,
Erinaceus europaeus	ENSEEUG00000013363	2 retrocopies	retro_eeur_63, retro_eeur_697,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Oryctolagus cuniculus	ENSOCUG00000013866	9 retrocopies	retro_ocun_1080, retro_ocun_1229, retro_ocun_1783, retro_ocun_1803, retro_ocun_1831, retro_ocun_327, retro_ocun_328, retro_ocun_557, retro_ocun_779,
Pongo abelii	ENSPPYG00000029483	1 retrocopy	retro_pabe_3478 ,
Tursiops truncatus	ENSTTRG00000007522	2 retrocopies	retro_ttru_1556, retro_ttru_694,