RetrogeneDB ID: retro_ptro_1216

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:21461381..21462345(-)
• Located in intron of: ENSPTRG00000030902

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF5L
• Ensembl ID: ENSPTRG00000002091
• Aliases: None
• Description: None

Sequence

>retro_ptro_1216
ATGAAATGAGTGCGTACCGAGGAGATCCAGATGGCAGTGTCCTGCTACCTCAAACGCTGGCATTACGTGGACTCTGACGG
TCCCCTGAAGCAAGGACTGCGGCTGCCACAGACTGCTGAAGAGTTGGCGGCCAATCTCACAGTACACAGAGAATCTCATT
GTGCCGACATAGTGTCTGCAGCCCCTTGCCAGGCAGAGCCCCAGCAATATGAAGTACAGTTTGGACGACTGCGGAATTTT
CTCATCGATTCTGATTCCCCGCATAGCCACGAAGTGATGCCTCTCCTTTATCCTCTCTTTGTCTGCCTCCATCTCAGCCT
GGTCCAGAACAGTCCAAAAAGTACAGTGGAAAGTTTTTACAGCCGCTTGCATGGAATGTTTCTGCAGAACGCTAGCCAGA
AGGACGTCATTGAGCAGCTACAGACCACTCAAACCATCCAGGACATCCTATCTAACTTCAAGCTTCGAGCATTCCTAGAT
AACAATTACGTGGTCCATCTCCAAGAAGACAGCTACAACTACCTTATCCACTACCTCCAAAGTGACAGCTATACTGCCCT
GTGCAAAATCCTCATCTTACATATTCATCTTGATGTGCAGCCTGCCAAGACAACAGACTAACAGCTGTATGCAAGTGGCA
GCTCCTCCCGCCGTGAGAACAATGACTTGGAGGCCCCTGATATGCCCAGCCCTATTCTGCCAGAACGATGCTGCCCTGGA
GGTCTTACAGGAGAGCATTAAGCAAGTCAAGGATGGGTCTCCCTCCCTCACTACCATCTGCTTCTATAACACCTAGCAGC
TGTTGAACACTGCAGAAATCTCCCCTGATAGCAAGCTGCTTGCTGCTGGGTTTGACAACTCCTGTATAAAACTTTGGAGC
TTACAATCCCAGAAGTTAAAATCAGAGTCCTGTCAAGTAGACATGTCCCGCATCCATTTGGCTTGTGATATTCTGGAGGA
GGAT

Alignment

ORF - retro_ptro_1216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.38 %
• Parental protein coverage: 55.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKRVRTEQIQMAVSCYLKRRQYVDSDGPLKQGLRLSQTAEEMAANLTVQSESGCANIVSAAPCQAEPQQY
          MK.VRTE.IQMAVSCYLKR..YVDSDGPLKQGLRL.QTAEE.AANLTV..ES.CA.IVSAAPCQAEPQQY
Retrocopy MK*VRTEEIQMAVSCYLKRWHYVDSDGPLKQGLRLPQTAEELAANLTVHRESHCADIVSAAPCQAEPQQY

Parental  EVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLQNASQKDVIEQL
          EVQFGRLRNFL.DSDS.HSHEVMPLLYPLFV.LHL.LVQNSPKSTVESFYSR.HGMFLQNASQKDVIEQL
Retrocopy EVQFGRLRNFLIDSDSPHSHEVMPLLYPLFVCLHLSLVQNSPKSTVESFYSRLHGMFLQNASQKDVIEQL

Parental  QTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQPAKRTDYQLY
          QTTQTIQDILSNFKLRAFLDN.YVV.LQEDSYNYLI.YLQSD..TALCK.L.LHIHLDVQPAK.TD.QLY
Retrocopy QTTQTIQDILSNFKLRAFLDNNYVVHLQEDSYNYLIHYLQSDSYTALCKILILHIHLDVQPAKTTD*QLY

Parental  ASGSSSRSENNGLEPPDMPSPIL-QNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISPD
          ASGSSSR.ENN.LE.PDMPSPIL.QN.AALEVLQESIK.VKDG.PSLTTICFY...NT.QLLNTAEISPD
Retrocopy ASGSSSRRENNDLEAPDMPSPIL>QNDAALEVLQESIKQVKDGSPSLTTICFY---NT*QLLNTAEISPD

Parental  SKLLAAGFDNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEE
          SKLLAAGFDNSCIKLWSL.S.KLKSE..QVD.SRIHLACDILEE.
Retrocopy SKLLAAGFDNSCIKLWSLQSQKLKSESCQVDMSRIHLACDILEED

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	0.23 RPM	6.24 RPM
SRP007412_cerebellum	0.07 RPM	11.36 RPM
SRP007412_heart	0.52 RPM	3.67 RPM
SRP007412_kidney	0.34 RPM	6.80 RPM
SRP007412_liver	0.29 RPM	8.58 RPM
SRP007412_testis	0.21 RPM	2.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1216 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1216 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1750

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034225	1 retrocopy	retro_btau_1300,
Callithrix jacchus	ENSCJAG00000010986	1 retrocopy	retro_cjac_4042,
Homo sapiens	ENSG00000135801	1 retrocopy	retro_hsap_1750,
Gorilla gorilla	ENSGGOG00000028544	1 retrocopy	retro_ggor_2253,
Pan troglodytes	ENSPTRG00000002091	1 retrocopy	retro_ptro_1216 ,
Rattus norvegicus	ENSRNOG00000018027	1 retrocopy	retro_rnor_509,