RetrogeneDB ID: retro_ptro_1504

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:25309037..25309487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA2
• Ensembl ID: ENSPTRG00000006536
• Aliases: None
• Description: iron-sulfur cluster assembly 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19857]

Sequence

>retro_ptro_1504
ATGGTTGCCGCCCAGGGGTTGTCCTTAAGGGCCGCGACGCAGACATCGGTCACTCCCTGGCCGAGGGGCAGGCTCCTCGC
GGCCTCCCTGGGACTCCGGGGCGTGTCCTCCAGCCCCGAGGCCGGCGACGGGCAGATCCGCCTCACGGACAGCTGCGTCC
AGAGGCTTCTGGAAATCACCAAAGGATCAGAATTCCTCAGGCTGCAGGTGGAGGGAGGTAGATGCTCCGGATTCCAGTAC
AGGTGTTCACTGGATACAGTTATCAACCCCGACCACAGGGTATTTGAACAGGGTGGGGCAAGAGTGGTGGTTGACTCTGA
TAGCTTAGCCGTCGCGAAAGGGGCCCAGGTGGACTTCAGCCAAGAACTGATCCGAAGCTCATTTCAAGTGTCAAACAATC
CTCAAGCACAGCAAGGCTGCTCCTGTGGGTCATCCTTCTCTGTCAAACTT

Alignment

ORF - retro_ptro_1504 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAWGSSLTAATQRAVTPWPRGRLLAASLGPQARREASSSSPEAGEGQIRLTDSCVQRLLEITEGSEFL
          M.AA.G.SL.AATQ..VTPWPRGRLLAASLG....R..SSS.PEAG.GQIRLTDSCVQRLLEIT.GSEFL
Retrocopy MVAAQGLSLRAATQTSVTPWPRGRLLAASLG---LRGVSSS-PEAGDGQIRLTDSCVQRLLEITKGSEFL

Parental  RLQVEGGGCSGFQYKFSLDTVINPDDRVFEQGGARVVVDSDSLAFVKGAQVDFSQELIRSSFQVLNNPQA
          RLQVEGG.CSGFQY..SLDTVINPD.RVFEQGGARVVVDSDSLA..KGAQVDFSQELIRSSFQV.NNPQA
Retrocopy RLQVEGGRCSGFQYRCSLDTVINPDHRVFEQGGARVVVDSDSLAVAKGAQVDFSQELIRSSFQVSNNPQA

Parental  QQGCSCGSSFSIKL
          QQGCSCGSSFS.KL
Retrocopy QQGCSCGSSFSVKL

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	0.02 RPM	7.61 RPM
SRP007412_cerebellum	0.00 RPM	9.68 RPM
SRP007412_heart	0.00 RPM	8.39 RPM
SRP007412_kidney	0.03 RPM	18.15 RPM
SRP007412_liver	0.00 RPM	10.08 RPM
SRP007412_testis	0.00 RPM	7.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1504 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1504 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1610
Macaca mulatta	retro_mmul_643

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068, retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504 ,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009,