RetrogeneDB ID: retro_ggor_2253

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:48599952..48600915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF5L
• Ensembl ID: ENSGGOG00000028544
• Aliases: None
• Description: None

Sequence

>retro_ggor_2253
ATGAAATGAGTGCCTACCGAGGAGATCCAGATGGCAGTGTCCTGCTACCTCAAACGCTGGCAGTACGTGGACTCAGACGG
TCCCCTGAAGCAAGGACTGCGGCTGCCACAGACTGCTGAAGAGTTGGCGGCCAATCTCACAGTACACAGAGAATCTCATT
GTGCCGACATAGTGTCTGCAGCCCCTTGCCAGGCAGAGCCCCAGCAATATGAAGTACAGTTTGGACGACTGCGGAATTTT
CTCATCGATTCTGATTCCCCGCATAGCCACGAAGTGATGCCTCTCCTTTATCCTCTCTTTGTCTGCCTCCATCTCAGCCT
GGTCCAGAACAGTCCAAAAAGTACAGTGGAAAGTTTTTACAGCCGCTTCCATGGAATGTTTCTGCAGAACTCTAGCCAGA
AGGACGTCATTGAGCAGCTACAGACCACTCAAACCATCCAGGACATCCTATCTAACTTCAAGCTTCAAGCATTCCTAGAT
AACAATTACGTGGTCCATCTCCAAGAAGACAGTTACAACTACCTTATCCACTACCTCCAAAGTGACAGCTATACTGCCCT
GTGCAAAATCCTCATCTTACATATTCATCTTGATGTGCAGCCTACCAAGACAACAGACTAACAGCTGTATGCAAGTGGCA
GCTCCTCCCGCAGTGAGAACAATGACTTGGAGGCCCCTGATATGCCCAGCCCTATTCTGCAGAACGATGCTGCCCTGGAG
GTCTTACAGGAGAGCATTAAGCAAGTCAAGGATGGGTCTCCCTCCCTCACTACCATCTGCTTCTATAACACCTAGCAGCT
GTTGAACACTGCAGAAATCTCCCCTGATAGCAAGCTGCTTGCTGCTGGGTTTGACAACTCCTGTATAAAACTCTGGAGCT
TACAATCCAAGAAGTTAAAATCAGAGTCCTGTCAAGTAGACATGTCCCGCATCCATTTGGCTTGTGATATTCTGGAGGAG
GAT

Alignment

ORF - retro_ggor_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 55.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKRVRTEQIQMAVSCYLKRRQYVDSDGPLKQGLRLSQTAEEMAANLTVQSESGCANIVSAAPCQAEPQQY
          MK.V.TE.IQMAVSCYLKR.QYVDSDGPLKQGLRL.QTAEE.AANLTV..ES.CA.IVSAAPCQAEPQQY
Retrocopy MK*VPTEEIQMAVSCYLKRWQYVDSDGPLKQGLRLPQTAEELAANLTVHRESHCADIVSAAPCQAEPQQY

Parental  EVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLQNASQKDVIEQL
          EVQFGRLRNFL.DSDS.HSHEVMPLLYPLFV.LHL.LVQNSPKSTVESFYSRFHGMFLQN.SQKDVIEQL
Retrocopy EVQFGRLRNFLIDSDSPHSHEVMPLLYPLFVCLHLSLVQNSPKSTVESFYSRFHGMFLQNSSQKDVIEQL

Parental  QTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQPAKRTDYQLY
          QTTQTIQDILSNFKL.AFLDN.YVV.LQEDSYNYLI.YLQSD..TALCK.L.LHIHLDVQP.K.TD.QLY
Retrocopy QTTQTIQDILSNFKLQAFLDNNYVVHLQEDSYNYLIHYLQSDSYTALCKILILHIHLDVQPTKTTD*QLY

Parental  ASGSSSRSENNGLEPPDMPSPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISPDS
          ASGSSSRSENN.LE.PDMPSPILQN.AALEVLQESIK.VKDG.PSLTTICFY...NT.QLLNTAEISPDS
Retrocopy ASGSSSRSENNDLEAPDMPSPILQNDAALEVLQESIKQVKDGSPSLTTICFY---NT*QLLNTAEISPDS

Parental  KLLAAGFDNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEE
          KLLAAGFDNSCIKLWSL.SKKLKSE..QVD.SRIHLACDILEE.
Retrocopy KLLAAGFDNSCIKLWSLQSKKLKSESCQVDMSRIHLACDILEED

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	0.14 RPM	15.25 RPM
SRP007412_cerebellum	0.04 RPM	18.32 RPM
SRP007412_heart	0.13 RPM	7.63 RPM
SRP007412_kidney	0.20 RPM	8.83 RPM
SRP007412_liver	0.24 RPM	15.69 RPM
SRP007412_testis	0.52 RPM	9.84 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2253 has 0 orthologous retrocopies within eutheria group .

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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,