RetrogeneDB ID: retro_pabe_2768

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:111795220..111795886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITFG2
• Ensembl ID: ENSPPYG00000004150
• Aliases: None
• Description: Integrin-alpha FG-GAP repeat-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RBH8]

Sequence

>retro_pabe_2768
GACGGAGATGGGTGTTGTGAATGGTGGTGGGCTACACAGACCGTGTGGTGCGAGCTTTTCGCTGGGAGGAGCTAGGTGAG
GGTCCTGAACATCTGACCGGGCAGCTGGTGTCCCTCAAGAAATGGTTGCTGGAGAGTCAGGTGGACAGCCTCTCAGTGAC
TCTGGGGCCGCTGGGTATTCCTGAACTGATGGTGTCTTAGCCAGGCTGTGCTTATGCAATTCTAATGTGTATGTGGAAAA
AGGACACAGGGTCCCCTCCTGCCTCTGAAGGGGTCATGGATGGCAGTAGGGAGACCCTAGCTGCCCGAGATGTGGTGCTG
CACCAGACATCTGGCAGTATCCACAACAAGAATATCTCCACTCACCTAATTGGTAACAACAAATAAGGCCATGGCACTGA
GAGTGGTGGCTCTGGCATCTTTGCCGTGAGCACACTGGATGGGATACTGAAGCTCATGGAGGAAGCAGACAAGCTGTTGT
GGTCAGCACAGGTGGTTCACCAGCTTTTCGCCCTGGAAAAATTGGGATGTCACTGGCAATGGGCATGAGGAGGTAGTTGC
ATGTGCCTGGGATGGACAGACATATATTATTGATCACAATCGCACTGTCATCCACTTCCAAGTGGATAAAAATATCCATG
CCTTTTGTGCAGGCCTGTATGCCTGC

Alignment

ORF - retro_pabe_2768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGDGCRE-LVVGYTDRVVRAFRWEELGEGPEHLTGQLVSLKKWMLEGQVDSLSVTLGPLGLPELMVSQPG
          DGDGC.E..VVGYTDRVVRAFRWEELGEGPEHLTGQLVSLKKW.LE.QVDSLSVTLGPLG.PELMVS.PG
Retrocopy DGDGCCE<MVVGYTDRVVRAFRWEELGEGPEHLTGQLVSLKKWLLESQVDSLSVTLGPLGIPELMVS*PG

Parental  CAYAILLCTWKKDTGSPPASEGPMDGSRETPAARDVVLHQTSGRIHNKNVSTHLTGNIKQGHGTESSGSG
          CAYAIL.C.WKKDTGSPPASEG.MDGSRET.AARDVVLHQTSG.IHNKN.STHL.GN.K.GHGTES.GSG
Retrocopy CAYAILMCMWKKDTGSPPASEGVMDGSRETLAARDVVLHQTSGSIHNKNISTHLIGNNK*GHGTESGGSG

Parental  LFALCTLDGTLKLMEEMEEADKLLWSVQVDHQLFALEKL-DVTGNGHEEVVACAWDGQTYIIDHNRTVVR
          .FA..TLDG.LKLMEE...ADKLLWS.QV.HQLFALEKL.DVTGNGHEEVVACAWDGQTYIIDHNRTV..
Retrocopy IFAVSTLDGILKLMEE---ADKLLWSAQVVHQLFALEKL>DVTGNGHEEVVACAWDGQTYIIDHNRTVIH

Parental  FQVDENIRAFCAGLYAC
          FQVD.NI.AFCAGLYAC
Retrocopy FQVDKNIHAFCAGLYAC

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	21.67 RPM
SRP007412_cerebellum	0.00 RPM	44.87 RPM
SRP007412_heart	0.00 RPM	6.53 RPM
SRP007412_kidney	0.00 RPM	23.14 RPM
SRP007412_liver	0.00 RPM	8.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2768 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2768 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2768 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3365
Gorilla gorilla	retro_ggor_2280

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000111203	1 retrocopy	retro_hsap_3365,
Gorilla gorilla	ENSGGOG00000010482	1 retrocopy	retro_ggor_2280,
Pongo abelii	ENSPPYG00000004150	1 retrocopy	retro_pabe_2768 ,