RetrogeneDB ID: retro_pabe_1468

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:68199708..68200047(+)
• Located in intron of: ENSPPYG00000008683

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5AL1
• Ensembl ID: ENSPPYG00000007907
• Aliases: None
• Description: eukaryotic translation initiation factor 5A-like 1 [Source:HGNC Symbol;Acc:17419]

Sequence

>retro_pabe_1468
AAGATCGTCGAGATGTCTACTTCGAGGACTGGCGAGCATGGCCATGCCAAGGTCCACCTGGTTGGTACTGACATCTTTAC
TGGGAAGAAATATGAAGATATCTGCCCGTCAACTCATAACATGGATGTCCCCAACATCAAAAGGAATGACTTCCAGCTGA
TTGGCATCCAGGATGGGCACCTATCACTGTTCCAGGACAGTGGGGAGGTGCAAGAGGACCTTCGTCTGCATGAGGGAGAC
CTTGGCTAGGAGACTGAGCAGAAGTACGGCTGTGGAGAAGAGATCCTGATCACGGTGCTGTCTGCCATGACCGAGGAGGC
AGCTGCTGCCATCAAGGCT

Alignment

ORF - retro_pabe_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEV
          KIVEMSTS.TG.HGHAKVHLVG.DIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDG.LSL.QDSGEV
Retrocopy KIVEMSTSRTGEHGHAKVHLVGTDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGHLSLFQDSGEV

Parental  REDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKA
          .EDLRL.EGDLG.E.EQKY.CGEEILITVLSAMTEEAA.AIKA
Retrocopy QEDLRLHEGDLG*ETEQKYGCGEEILITVLSAMTEEAAAAIKA

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	0.11 RPM	96.43 RPM
SRP007412_cerebellum	0.00 RPM	85.12 RPM
SRP007412_heart	0.00 RPM	58.76 RPM
SRP007412_kidney	0.36 RPM	138.59 RPM
SRP007412_liver	0.03 RPM	127.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1468 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1468 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1788
Pan troglodytes	retro_ptro_1198

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Parental genes homology:

Parental genes homology involve 7 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,
Macaca mulatta	ENSMMUG00000006206	1 retrocopy	retro_mmul_1379,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468 ,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Rattus norvegicus	ENSRNOG00000016478	3 retrocopies	retro_rnor_1627, retro_rnor_1947, retro_rnor_671,