RetrogeneDB ID: retro_ptro_2577

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:141011078..141011390(+)
• Located in intron of: ENSPTRG00000039273

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSPTRG00000006482
• Aliases: None
• Description: Enhancer of rudimentary homolog [Source:UniProtKB/TrEMBL;Acc:H2Q8I5]

Sequence

>retro_ptro_2577
ATGTCTCACACCATTTTGCTGATACAGACTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTACGAATCTGTGAATGA
ATGCATGGAAGGCGTTTGTAAAATGTATGAAGACATGTGAAAAGAATGAATCCCAACAGTCCCTCTATCAAGTATGACAT
CAGTCAGTTGTTTGATTTCATCAATGATCTGGCAGACCTCAGCTGCCTGGTTTACCGAGCTGATACCCAGACATACCAGC
CTTATAAAAAAAGACTGGATTAAAGAGAAGATCTACATGCTTCTTCATCGGCAGGCTCAACAGGCTGATAAA

Alignment

ORF - retro_ptro_2577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE-HLKRMNPNSPSITYDISQLFDFIDDLADLSC
          MSHTILL.Q.TKRPEGRTYADYESVNECMEGVCKMYE..H.KRMNPNSPSI.YDISQLFDFI.DLADLSC
Retrocopy MSHTILLIQTTKRPEGRTYADYESVNECMEGVCKMYED<HVKRMNPNSPSIKYDISQLFDFINDLADLSC

Parental  LVYRADTQTYQPY-NKDWIKEKIYVLLRRQAQQAGK
          LVYRADTQTYQPY..KDWIKEKIY.LL.RQAQQA.K
Retrocopy LVYRADTQTYQPY>KKDWIKEKIYMLLHRQAQQADK

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	0.68 RPM	37.59 RPM
SRP007412_cerebellum	0.18 RPM	58.18 RPM
SRP007412_heart	0.09 RPM	34.65 RPM
SRP007412_kidney	0.03 RPM	49.74 RPM
SRP007412_liver	0.00 RPM	63.24 RPM
SRP007412_testis	0.32 RPM	254.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2577 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Gorilla gorilla	ENSGGOG00000004751	2 retrocopies	retro_ggor_2424, retro_ggor_2553,
Microcebus murinus	ENSMICG00000009623	1 retrocopy	retro_mmur_74,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Nomascus leucogenys	ENSNLEG00000001514	2 retrocopies	retro_nleu_1128, retro_nleu_1604,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Pan troglodytes	ENSPTRG00000006482	2 retrocopies	retro_ptro_2433, retro_ptro_2577 ,
Sorex araneus	ENSSARG00000005558	11 retrocopies	retro_sara_114, retro_sara_127, retro_sara_151, retro_sara_221, retro_sara_251, retro_sara_295, retro_sara_298, retro_sara_490, retro_sara_56, retro_sara_58, retro_sara_66,