RetrogeneDB ID: retro_ptro_3275

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:148939437..148939947(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSPTRG00000001380
• Aliases: None
• Description: None

Sequence

>retro_ptro_3275
GGTTCTGAGTCAGAGACACCTGGTGAGAGACTGCGGAGGGGACAGGCACTTCGAGATCAAATGCTTAAGTATCCAGATAG
TCACCAGCCCAGGATCTTGAGGGGGTCTTGGAGAGTGATGCAAGAAGTGAATCCCCCAAACCAGCACCAGACTGAGGCTC
CCAGAGACCATTTCGTAGGTTTGATGACGTATGGCCTGTGGACCCCCATCCTAGAACCAGAGAGGACAATGATCTTGATT
CCCGGGTTTCCCAGGAGCGTCTTGGCCCGGTTCTACAGCCCCAGCCCAGATCTATTTCAAGAGCATCTCTGTGACCAAAA
TCACTAAGCCAGATGGGATAGTGGAGGAGCGCTGGACTGTCATGGACAGTGAGGGCCAGACAGAGACCGCAGTAACCCAA
CACGAAGCAGATAGCAGTCCTAGGATGATCCAGAATCACCAAGACCTCCAGCCCTGGATGATGCCTTCTCCATCCTGGAC
TTATTCCTAGGATGTTGGTTCCAGTCCCGG

Alignment

ORF - retro_ptro_3275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPESETPGERLREGQTLRDSMLKYPDSHQPRIFGG-VLESDARSESPQPAPDWGSQRPFHRFDDVWPMDP
          G.ESETPGERLR.GQ.LRD.MLKYPDSHQPRI..G.VLESDARSESP.PAPD.GSQRPF.RFDDVWP.DP
Retrocopy GSESETPGERLRRGQALRDQMLKYPDSHQPRILRG<VLESDARSESPKPAPD*GSQRPFRRFDDVWPVDP

Parental  HPRTREDNDLDSQVSQEGLGPVLQPQPKS-YFKSISVTKITKPDGIVEERRTVVDSEGRTETTVTRHEAD
          HPRTREDNDLDS.VSQE.LGPVLQPQP.S.YFKSISVTKITKPDGIVEER.TV.DSEG.TET.VT.HEAD
Retrocopy HPRTREDNDLDSRVSQERLGPVLQPQPRS<YFKSISVTKITKPDGIVEERWTVMDSEGQTETAVTQHEAD

Parental  SSPR-GDPESPRPPALDDAFSILDLFLGRWFRSR
          SSPR..DPESPRPPALDDAFSILDLFLG.WF.SR
Retrocopy SSPR<DDPESPRPPALDDAFSILDLFLGCWFQSR

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	46.85 RPM
SRP007412_cerebellum	0.00 RPM	53.20 RPM
SRP007412_heart	0.03 RPM	76.36 RPM
SRP007412_kidney	0.00 RPM	54.76 RPM
SRP007412_liver	0.00 RPM	60.75 RPM
SRP007412_testis	0.00 RPM	64.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3275 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3275 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4912

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275 ,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,