RetrogeneDB ID: retro_ptro_315

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:78728726..78729336(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSPTRG00000015161
• Aliases: None
• Description: nitrilase family, member 2 [Source:HGNC Symbol;Acc:29878]

Sequence

>retro_ptro_315
GCAACTTTCCACTTGGCCCTCATCCAGCTTCAAGTTTCTTCATCAAATCAGATAACAACACTCGAGCTTGTAGCCTTGTC
CGGGAGACAGCAACGCAAGGAGCCAAAATGGTTTCTTTGTTGGAATGCTTTAATTCTCCATATGGCACAAAATATTTTCC
TGAATATGCAGCGAAAATTCCTGGTAAATCCACACAGAAGCTTTCTGAAGTAGCAAAGGAATACAGCCTCACTAGAGGTT
CCATCCCTGAAGAGGATGCTGAGAAATTAGATAACACCTGTGCTGTGTTTGCACCTCATGGAACTTTACTAGTAAAGCAC
AGAAAGGTCCATCTGCTTAACACTGGTGTTCCTGGAAAAATGACGTTTCAAGAATCCACAATGTTGAGTCCGGGCAACAG
TTTCTCCACATTTGATACTCCTTACTGCAGAATGAGTCGGGGCATCTGCTATGACACTGGTTTGCAGAGCTTGCACAAAT
CTACACACGGAAAGGCTGCCAGCTGTTGGTTTATCCAGGGGCTTTCAGTTTGACCACTGGACCAGCCCACTGGGAATTGC
TTCAGGCTCTTGATAATCAGGTGTATGTGGCCACATTCTCCTGCCCAAGA

Alignment

ORF - retro_ptro_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.83 %
• Parental protein coverage: 75.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAFRLALIQLQISS-IKSDNVTRACSFIREAATQGAKIVSLPECFNSPYGTKYFPEYAEKIPGESTQKLC
          ..F.LALIQLQ.SS.IKSDN.TRACS..RE.ATQGAK.VSL.ECFNSPYGTKYFPEYA.KIPG.STQKL.
Retrocopy ATFHLALIQLQVSS<IKSDNNTRACSLVRETATQGAKMVSLLECFNSPYGTKYFPEYAAKIPGKSTQKLS

Parental  EVAKECSIYLIGGSIPEEDAGKLYNTCAVFGPDGTLLAKYRKIHLFDIDVPGKITFQESKTLSPGDSFST
          EVAKE.S..L..GSIPEEDA.KL.NTCAVF.P.GTLL.K.RK.HL....VPGK.TFQES..LSPG.SFST
Retrocopy EVAKEYS--LTRGSIPEEDAEKLDNTCAVFAPHGTLLVKHRKVHLLNTGVPGKMTFQESTMLSPGNSFST

Parental  FDTPYCRVGLGICYDMR-FAELAQIYAQRGCQLLVYPGAFNLTTGPAHWELLQRSRAVDNQVYVATASPA
          FDTPYCR...GICYD...FAELAQIY...GCQLLVYPGAF.LTTGPAHWELLQ...A.DNQVYVAT.S..
Retrocopy FDTPYCRMSRGICYDTG<FAELAQIYTRKGCQLLVYPGAFSLTTGPAHWELLQ---ALDNQVYVATFSCP

Parental  R
          R
Retrocopy R

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	7.36 RPM
SRP007412_cerebellum	0.00 RPM	7.67 RPM
SRP007412_heart	0.03 RPM	12.50 RPM
SRP007412_kidney	0.08 RPM	70.61 RPM
SRP007412_liver	0.00 RPM	66.84 RPM
SRP007412_testis	0.00 RPM	2.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_315 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_315 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_411
Gorilla gorilla	retro_ggor_406
Macaca mulatta	retro_mmul_505
Callithrix jacchus	retro_cjac_3014

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315 ,