RetrogeneDB ID: retro_hsap_1750

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:33825234..33826200(+)
• Located in intron of: ENSG00000205045

Retrocopy information

• Ensembl ID: ENSG00000267369
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF5L
• Ensembl ID: ENSG00000135801
• Aliases: TAF5L, PAF65B
• Description: TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa [Source:HGNC Symbol;Acc:17304]

Sequence

>retro_hsap_1750
ATGAAATGAGTGCGTACCGAGGAGATCCAGATGGCAGTGTCCTGCTACCTCAAACGCTGGCAGTACGTGGACTCAGACGG
TCCCCTGAAGCAAGGACTGCGGCTGCCACAGACTGCTGAAGAGTTGGCGGCCAATCTCACGGTACACAGAGAATCTCATT
GTGCCGACATAGTGTCTGCAGTCCCTTGCCAGGCAGAGCCCCAGCAATATGAAGTACAGTTTGGACGACTGCGGAATTTT
CTCATCGATTCTGATTCCCCGCATAGCCACGAAGTGATGCCTCTCCTTTATCCTCTCTTTGTCTGCCTCCATCTCAGCCT
GGTCCAGAACAGTCCAAAAAGTACAGTGGAAAGTTTTTACAGCCGCTTCCATGGAATGTTTCTGCAGAAAGCTAGCCAGA
AGGGCGTCATTGAGCAGCTACAGACCACTCAAACCATCCAGGACATCCTATCTAACTTCAAGCTTCGAGCATTCCTAGAT
AACAATTACGTGGTCCATCTCCAAGAAGACAGCTACAACTACCTTATCCACTACCTCCAAAGTGACAGCTATACTGCCCT
GTGCAAAATGTTTATCTTACTTATTCATCTTGATGTGCAGCCTGCCAAGACAACAGACTAACAGCTGTATGCAAGTGGCA
GCTCCTCCCGCAGTGAGAACAATTACTTGGAGGCCCCTGATATGCCCAGCCCTATTCTGCAGAACGATGCTGCCCTGGAG
GTCTTACAGGAGCGCATTAAGCAAGTCAAGGATGGGTGTCCCTCCCTCACTACCGTCTGCTTCTATAACACCTAGCAGCT
GTTGAACACTGCAGAAATCTCCCCTGATAGCAAGCTGCTTGCTGCTGGGTTTGACAACTCCTGTATAAAACTTTGGAGCT
TACAATCCAGGAAGTTAAAATCAGAGTCCTGTCAAGTAGACATGTCCCGCATCCATTTGGCTTGTGATATTCTGGAGGAG
GATGTG

Alignment

ORF - retro_hsap_1750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKRVRTEQIQMAVSCYLKRRQYVDSDGPLKQGLRLSQTAEEMAANLTVQSESGCANIVSAAPCQAEPQQY
          MK.VRTE.IQMAVSCYLKR.QYVDSDGPLKQGLRL.QTAEE.AANLTV..ES.CA.IVSA.PCQAEPQQY
Retrocopy MK*VRTEEIQMAVSCYLKRWQYVDSDGPLKQGLRLPQTAEELAANLTVHRESHCADIVSAVPCQAEPQQY

Parental  EVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLQNASQKDVIEQL
          EVQFGRLRNFL.DSDS.HSHEVMPLLYPLFV.LHL.LVQNSPKSTVESFYSRFHGMFLQ.ASQK.VIEQL
Retrocopy EVQFGRLRNFLIDSDSPHSHEVMPLLYPLFVCLHLSLVQNSPKSTVESFYSRFHGMFLQKASQKGVIEQL

Parental  QTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQPAKRTDYQLY
          QTTQTIQDILSNFKLRAFLDN.YVV.LQEDSYNYLI.YLQSD..TALCK...L.IHLDVQPAK.TD.QLY
Retrocopy QTTQTIQDILSNFKLRAFLDNNYVVHLQEDSYNYLIHYLQSDSYTALCKMFILLIHLDVQPAKTTD*QLY

Parental  ASGSSSRSENNGLEPPDMPSPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISPDS
          ASGSSSRSENN.LE.PDMPSPILQN.AALEVLQE.IK.VKDG.PSLTT.CFY...NT.QLLNTAEISPDS
Retrocopy ASGSSSRSENNYLEAPDMPSPILQNDAALEVLQERIKQVKDGCPSLTTVCFY---NT*QLLNTAEISPDS

Parental  KLLAAGFDNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEEV
          KLLAAGFDNSCIKLWSL.S.KLKSE..QVD.SRIHLACDILEE.V
Retrocopy KLLAAGFDNSCIKLWSLQSRKLKSESCQVDMSRIHLACDILEEDV

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
bodymap2_adipose	0.52 RPM	21.39 RPM
bodymap2_adrenal	4.91 RPM	31.65 RPM
bodymap2_brain	0.09 RPM	18.17 RPM
bodymap2_breast	1.56 RPM	19.88 RPM
bodymap2_colon	0.00 RPM	15.24 RPM
bodymap2_heart	0.15 RPM	14.93 RPM
bodymap2_kidney	0.04 RPM	13.36 RPM
bodymap2_liver	0.04 RPM	13.43 RPM
bodymap2_lung	2.95 RPM	14.93 RPM
bodymap2_lymph_node	10.60 RPM	21.40 RPM
bodymap2_ovary	0.83 RPM	21.28 RPM
bodymap2_prostate	0.07 RPM	31.40 RPM
bodymap2_skeletal_muscle	0.00 RPM	10.31 RPM
bodymap2_testis	0.28 RPM	19.10 RPM
bodymap2_thyroid	0.34 RPM	23.80 RPM
bodymap2_white_blood_cells	6.67 RPM	30.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1750 was not detected

EST

No EST(s) were mapped for retro_hsap_1750 retrocopy.

TSS

No TSS is located nearby retro_hsap_1750 retrocopy 5' end.

Lab

retro_hsap_1750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1750 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1216

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.46 RPM
CEU_NA11843	1.45 RPM
CEU_NA11930	5.08 RPM
CEU_NA12004	2.54 RPM
CEU_NA12400	4.77 RPM
CEU_NA12751	2.94 RPM
CEU_NA12760	4.90 RPM
CEU_NA12827	4.39 RPM
CEU_NA12872	1.12 RPM
CEU_NA12873	3.16 RPM
FIN_HG00183	8.62 RPM
FIN_HG00277	5.10 RPM
FIN_HG00315	2.43 RPM
FIN_HG00321	5.08 RPM
FIN_HG00328	4.64 RPM
FIN_HG00338	2.55 RPM
FIN_HG00349	5.46 RPM
FIN_HG00375	4.50 RPM
FIN_HG00377	5.90 RPM
FIN_HG00378	4.14 RPM
GBR_HG00099	7.03 RPM
GBR_HG00111	8.92 RPM
GBR_HG00114	6.36 RPM
GBR_HG00119	8.53 RPM
GBR_HG00131	6.73 RPM
GBR_HG00133	8.80 RPM
GBR_HG00134	9.61 RPM
GBR_HG00137	13.58 RPM
GBR_HG00142	2.78 RPM
GBR_HG00143	6.89 RPM
TSI_NA20512	10.60 RPM
TSI_NA20513	6.00 RPM
TSI_NA20518	2.89 RPM
TSI_NA20532	6.19 RPM
TSI_NA20538	5.44 RPM
TSI_NA20756	7.74 RPM
TSI_NA20765	7.44 RPM
TSI_NA20771	6.07 RPM
TSI_NA20786	2.28 RPM
TSI_NA20798	6.70 RPM
YRI_NA18870	10.43 RPM
YRI_NA18907	4.30 RPM
YRI_NA18916	1.39 RPM
YRI_NA19093	5.49 RPM
YRI_NA19099	4.63 RPM
YRI_NA19114	2.96 RPM
YRI_NA19118	5.97 RPM
YRI_NA19213	7.46 RPM
YRI_NA19214	8.83 RPM
YRI_NA19223	7.62 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).