RetrogeneDB ID: retro_ptro_1198

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:77123706..77124075(+)
• Located in intron of: ENSPTRG00000009702

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A
• Ensembl ID: ENSPTRG00000008674
• Aliases: None
• Description: eukaryotic translation initiation factor 5A [Source:HGNC Symbol;Acc:3300]

Sequence

>retro_ptro_1198
GGCTTTGTGGTACTCAAAGGCCGGCCACGTAAGATCGTCGAGATGTCTACTTCGATGACTGGCAAGCATGGCCATGCCAA
GGTCCACCTGGTTGGTACTGACATCTTTACTGGGAAGAAATATGGAGATATCTGCCTGTCAATTCATAACATGGATGTCC
CCAGCATCAAAAGGAATGACTTCCAGCTGATTGGCATCCAGGATGGGCACCTATCACTGCTCCAGGACAGCATGGAGGTG
CGAGAGGACCTTCGTCTGCATGAGGGAGACCTTGTCAAAGAGACTGAGCAGAAGTACAGCTGTGGAGAAGAGATCCTGAT
CATGGTGCTGTCTGCCATGACCGAGGAGGCAGCTGCTGCAATCAAGGCT

Alignment

ORF - retro_ptro_1198 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 66.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGY
          GFVVLKGRP.KIVEMSTS.TGKHGHAKVHLVG.DIFTGKKY.DIC.S.HNMDVP.IKRNDFQLIGIQDG.
Retrocopy GFVVLKGRPRKIVEMSTSMTGKHGHAKVHLVGTDIFTGKKYGDICLSIHNMDVPSIKRNDFQLIGIQDGH

Parental  LSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKA
          LSLLQDS.EVREDLRL.EGDL.KE.EQKY.CGEEILI.VLSAMTEEAA.AIKA
Retrocopy LSLLQDSMEVREDLRLHEGDLVKETEQKYSCGEEILIMVLSAMTEEAAAAIKA

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	113.09 RPM
SRP007412_cerebellum	0.00 RPM	78.72 RPM
SRP007412_heart	0.00 RPM	76.57 RPM
SRP007412_kidney	0.00 RPM	130.79 RPM
SRP007412_liver	0.00 RPM	257.98 RPM
SRP007412_testis	0.00 RPM	105.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1198 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1198 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1788
Pongo abelii	retro_pabe_1468

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132507	3 retrocopies	retro_hsap_1788, retro_hsap_2004, retro_hsap_9,
Gorilla gorilla	ENSGGOG00000012032	2 retrocopies	retro_ggor_1448, retro_ggor_159,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Otolemur garnettii	ENSOGAG00000014230	1 retrocopy	retro_ogar_2414,
Pan troglodytes	ENSPTRG00000008674	3 retrocopies	retro_ptro_1198 , retro_ptro_442, retro_ptro_504,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Sus scrofa	ENSSSCG00000017939	1 retrocopy	retro_sscr_1204,
Tursiops truncatus	ENSTTRG00000009783	1 retrocopy	retro_ttru_1526,