RetrogeneDB ID: retro_ptro_1681

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:228809817..228810449(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLX
• Ensembl ID: ENSPTRG00000009208
• Aliases: None
• Description: None

Sequence

>retro_ptro_1681
AAGGTGGAGTACATCTACAGCTACAAAAGCTCAGACCTCAAGTATTTTATAGAAAGCACCCACAATGGGACAGTAGTGTC
TAGAGCTAATAGCATCGGTTCCACCAGTGCCTCTTCCATCCCCAACACAGATGAGGAGGACAGTGATTACCACCAAGAGT
CCTACAAGGACCAGTAGTGGTGAGCACACACTGAGGCTGAGCAGAAGAGGAAGGATGTCATCAAGAGAGGCTGTGATGAC
CTTCAGACCATCATCCCCACATGCCAGCAGCAGGACTCCTGCATTGGCTCCCGAAAGCTCAGCAAAGCCATCGTTCTACA
AAAGACCATTGACTACACTCAGTTTTTGCACAAGGAGAAGAAAATGCAGGAGGAGGAGGTGTCCACACTATGCAAGGACC
TCACAGCCCTAAAGATCATGAAAGGGAACTATAAGCAGATTGTGAAGGCACACCAGGACAACCCCCATGAGGGGAGGACC
AGGCCTCTGACCAAGTCAAGGTCAGTGTGTTTCGAGGTATCATGGACTCCCTGTTCCAGTCCTTCAATGCCTTCATCTCT
GTGACCAGCTTCTAGGAGCTGTCAGCCTGTGTCTTCAGCTAGATTGAGGAGCACTGCAAGCCACAGGCCATG

Alignment

ORF - retro_ptro_1681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 72.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVEYAYSDNSLDPGLFVESTRKGSVVSRANSIGSTSASSVPNTDDEDSDYHQEAYKESYKDRRRRAHTQA
          KVEY.YS..S.D...F.EST..G.VVSRANSIGSTSASS.PNTD.EDSDYHQ....ESYKD....AHT.A
Retrocopy KVEYIYSYKSSDLKYFIESTHNGTVVSRANSIGSTSASSIPNTDEEDSDYHQ----ESYKDQ*W*AHTEA

Parental  EQKRRDAIKRGYDDLQTIVPTCQQQDFSIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDVTA
          EQKR.D.IKRG.DDLQTI.PTCQQQD..IGS.KLSKAIVLQKTIDY.QFLHKEKK.QEEEVSTL.KD.TA
Retrocopy EQKRKDVIKRGCDDLQTIIPTCQQQDSCIGSRKLSKAIVLQKTIDYTQFLHKEKKMQEEEVSTLCKDLTA

Parental  LKIMKVNYEQIVKAHQDNPHE-GEDQVSDQVKFNVFQGIMDSLFQSFNASISVASFQELSACVFSWIEEH
          LKIMK.NY.QIVKAHQDNPHE.GEDQ.SDQVK..VF.GIMDSLFQSFNA.ISV.SF.ELSACVFS.IEEH
Retrocopy LKIMKGNYKQIVKAHQDNPHE<GEDQASDQVKVSVFRGIMDSLFQSFNAFISVTSF*ELSACVFS*IEEH

Parental  CKPQTL
          CKPQ..
Retrocopy CKPQAM

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	0.00 RPM	15.71 RPM
SRP007412_cerebellum	0.00 RPM	17.60 RPM
SRP007412_heart	0.00 RPM	24.86 RPM
SRP007412_kidney	0.00 RPM	32.32 RPM
SRP007412_liver	0.00 RPM	28.87 RPM
SRP007412_testis	0.00 RPM	9.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1681 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1681 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2216
Gorilla gorilla	retro_ggor_1748
Pongo abelii	retro_pabe_2087

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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	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681 ,