RetrogeneDB ID: retro_ptro_1000

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:31910974..31911697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSPTRG00000013952
• Aliases: None
• Description: None

Sequence

>retro_ptro_1000
ATGGCGGAGTATCCAGCCTCCATCTTTGGCACCGAGAAAGTCAACTGTTCATTTGATTTCAAAATTGGAGCATGTCTTCA
TGGAGACAGGTGCTCTTGGTTGCACCATAAACCGATGTTTAGCCAGACCATTGCCCTCTTGAACATTTACTGTACCCCTC
AAAACGCTTCCCAGTCGGCCGACGGTTTGCGCTGTGCCGTGAGCGATGTTGAGGTGCAGGAACACTATGATGAATTTTTT
GAGGAGGTTTTTATAGAACTGGGGGAGAAGTATGGGGAAGTTGAGGAGATGAACGTCTGTGACAACCTGGGAGACCACCT
GATGGGGAACGTGTACTTCAAGCTTCCCCGTGAGGAAGATGCGGAAAAGGCTGTGATTGACTTGAACAACCGTTGGTTTA
ACGGACAGCCGATCCACGCCGAGCTGTCACCTGTGACGGACTTCAGGGGAGCCTGATGCCGTCAGTATGAGATGGGAGAA
TGCACACGAGGCGGCTTCTGCAACTTCATGCATTTGAAGCCCATTTCCAGAGAGCTGCGGCGGGAGCTGTGTGGGCAGCG
TCCCAAGAAGCATAGATCAAGATCCCGATCCCGGGAGCGTCGTTCTCGGTCTGGAGACCGTGGTCATGGCGATGGCGGTG
GCGGTGGCGGTGGCCCAGGCGGCGGCGGCCGACGGGAGCGTGACAGGAGGCGGTTGAGAGATCGTGAAAGATCTGGGCGA
TTC

Alignment

ORF - retro_ptro_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEYLASIFGTEKDKVNCSFYFKIGACRHGDRCSRLHNKPTFSQTILIQNIYRNPQNSAQTADGSHCAVS
          MAEY.ASIFGTEK..VNCSF.FKIGAC.HGDRCS.LH.KP.FSQTI...NIY..PQN..Q.ADG..CAVS
Retrocopy MAEYPASIFGTEK--VNCSFDFKIGACLHGDRCSWLHHKPMFSQTIALLNIYCTPQNASQSADGLRCAVS

Parental  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI
          DVE.QEHYDEFFEEVF.E..EKYGEVEEMNVCDNLGDHL.GNVY.K..REEDAEKAVIDLNNRWFNGQPI
Retrocopy DVEVQEHYDEFFEEVFIELGEKYGEVEEMNVCDNLGDHLMGNVYFKLPREEDAEKAVIDLNNRWFNGQPI

Parental  HAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELYGRRRKKHRSRSRSRERRSRSRDRG
          HAELSPVTDFR.A.CRQYEMGECTRGGFCNFMHLKPISRELRREL.G.R.KKHRSRSRSRERRSRS.DRG
Retrocopy HAELSPVTDFRGA*CRQYEMGECTRGGFCNFMHLKPISRELRRELCGQRPKKHRSRSRSRERRSRSGDRG

Parental  RGGGGGGGGGGGG---RERDRRRSRDRERSGRF
          ...........GG...RERDRRR.RDRERSGRF
Retrocopy XXXXXXXXXXPGGGGRRERDRRRLRDRERSGRF

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	0.05 RPM	30.92 RPM
SRP007412_cerebellum	0.11 RPM	72.49 RPM
SRP007412_heart	0.06 RPM	31.59 RPM
SRP007412_kidney	0.18 RPM	52.46 RPM
SRP007412_liver	0.10 RPM	83.34 RPM
SRP007412_testis	2.85 RPM	79.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1000 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1000 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1478
Gorilla gorilla	retro_ggor_150
Pongo abelii	retro_pabe_1227

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013835	1 retrocopy	retro_mmur_614,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pan troglodytes	ENSPTRG00000013952	2 retrocopies	retro_ptro_1000 , retro_ptro_549,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Tupaia belangeri	ENSTBEG00000000453	2 retrocopies	retro_tbel_2115, retro_tbel_963,
Vicugna pacos	ENSVPAG00000002856	1 retrocopy	retro_vpac_489,