RetrogeneDB ID: retro_ptro_2764

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:71477631..71478006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHRAC1
• Ensembl ID: ENSPTRG00000020621
• Aliases: None
• Description: chromatin accessibility complex 1 [Source:HGNC Symbol;Acc:13544]

Sequence

>retro_ptro_2764
TGGGCAAAGACAAGTGCAGGGAGCAGCGGCTCCTCTTGCTGTCCCTGTCTCACATCCGGTCATCATGAAGAGTTCTCCCA
TGGTGTTGTGCATCAACCTCGAGGTGCTCCTGGCCAAGGCCACACAACTCTTTGTTAAGTCTCTAACCATCTATTCCTAC
AGTCATGGCAGTGGAAAGAAGAAAGCACTAACAGTAATTTAGCAAATACAGCAGAGGAATCAGAAAATTTTCAGTTTCTT
GAAGGTGTATTATTGCCAAAGAAGGTTTCCACTAGTAAATACCTGAAAGTTCTTAAAGAGGAAAGGAGGGAAGAAGAAGA
TGAGGAGGAGGGGTAGAATGACTGTGATGGTGAAAGTGATGTTGATGAAGGTGAA

Alignment

ORF - retro_ptro_2764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.64 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WVKTRGG-EQRLRFLPL-RIR-VIMKSSPHVSSINQEALVLTAKATELFVQCLATYSYRHGSGKEKKVL-
          W.KT..G.EQRL..L.L..IR.VIMKSSP.V..IN.E..VL.AKAT.LFV..L..YS.....G..KK...
Retrocopy WAKTSAG<EQRLLLLSLSHIR<VIMKSSPMVLCINLE--VLLAKATQLFVKSLTIYS--YSHGSGKKKA<

Parental  TYSDLANTAQQSETFQFLADIL-PKKILASKYLKMLKEEKREEDEND---ND--NESDHDEAD
          T.S.LANTA..SE.FQFL...L.PKK...SKYLK.LKEE.REE.......ND...ESD.DE..
Retrocopy TNSNLANTAEESENFQFLEGVLLPKKVSTSKYLKVLKEERREEEDEEEG*NDCDGESDVDEGE

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	0.07 RPM	1.81 RPM
SRP007412_cerebellum	0.14 RPM	1.61 RPM
SRP007412_heart	0.12 RPM	1.49 RPM
SRP007412_kidney	0.10 RPM	3.19 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2764 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2764 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005017	1 retrocopy	retro_amel_1736,
Cavia porcellus	ENSCPOG00000010427	5 retrocopies	retro_cpor_1545, retro_cpor_721, retro_cpor_722, retro_cpor_723, retro_cpor_724,
Loxodonta africana	ENSLAFG00000001188	1 retrocopy	retro_lafr_932,
Monodelphis domestica	ENSMODG00000000756	2 retrocopies	retro_mdom_1379, retro_mdom_355,
Ochotona princeps	ENSOPRG00000008780	2 retrocopies	retro_opri_636, retro_opri_726,
Pan troglodytes	ENSPTRG00000020621	1 retrocopy	retro_ptro_2764 ,
Ictidomys tridecemlineatus	ENSSTOG00000008105	1 retrocopy	retro_itri_358,