RetrogeneDB ID: retro_ptro_3092

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:19045352..19046130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS1
• Ensembl ID: ENSPTRG00000009992
• Aliases: HAUS1, CCDC5
• Description: HAUS augmin-like complex, subunit 1 [Source:HGNC Symbol;Acc:25174]

Sequence

>retro_ptro_3092
GGAGATCATCCCATTCCACAGTATGAGGTGAACCCACGGACCACAGAGATTTTACATCACCTTTCAGAACACAACAGGTC
CAGGACAGGGATGTCTACCTGGTAATAGAGGACTTGAAGCAGAAAGCAAGTGAATACCAGTCAGAAGCCAAGTATCTCCA
AGACCTTCTCATGGAGAGTGTGAATTTTTTCCCCTGCCAATCTCTCTAGCACTGGTTCCAGGTATCTGAATGCTTTGGTT
GGCAGTGCGGTGGCCCTTGAAACGAAGGATGCCTCACTAACTAGTTTTATCCCTGTAGTGAATGATTTGACCTCTTACCT
CTTTCGTACCAAATCCAAAAGTGAAGAAATCAAGATTGAACTGGAAAAATTTGAAAAAAAATCTAACTGCAACTTTAGTA
TTAGAAAAATGTCTACAAGAGGATCTCAAGAAAGCAGAGTTGCATCTGTCTACAGAAAGGGCCAAAGTTGATAATCGTCA
TCAGAGCATGGACTTTCTAAAACCAAAGTCAGTGGAATTCAGATTTGGAATCAAGGCTGCAGAGGGAGCAACTTTCAGCC
AGAGGCATGGATGCTTCTCTGTCTCATCAGTCCCTAGTAGCACTGTCAGAGAAACTGGCAAAATTAAAACAACAGACTAT
ACCTTTGAAGAAAAAATTGGAGTCCTAGTTAGATTTAATGCCGAATCCATCCTTGCTCAAGTGAAAATTGAAGAAGCAGA
GCGAGAATTAGATAGCATTGAAGCTGAACTTACAAGAAGAGTAGACATGATGGAACTG

Alignment

ORF - retro_ptro_3092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 93.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GDHPIPQYEVNPRTTEILHHLSERNR-VRDRDVYLVIEDLKQKASEYESEAKYLQDLLMESVN-FSPANL
          GDHPIPQYEVNPRTTEILHHLSE.NR.V.DRDVYLVIEDLKQKASEY.SEAKYLQDLLMESVN.FSPANL
Retrocopy GDHPIPQYEVNPRTTEILHHLSEHNR<VQDRDVYLVIEDLKQKASEYQSEAKYLQDLLMESVN>FSPANL

Parental  SSTGSRYLNALVDSAVALETKDTSLASFIPAVNDLTSDLFRTKSKSEEIKIELEKLEKNLTATLVLEK-C
          SSTGSRYLNALV.SAVALETKD.SL.SFIP.VNDLTS.LFRTKSKSEEIKIEL..............K.C
Retrocopy SSTGSRYLNALVGSAVALETKDASLTSFIPVVNDLTSYLFRTKSKSEEIKIELXXXXXXSNCNFSIRK>C

Parental  LQEDVKKAELHLSTERAKVDNRRQNMDFLKAKSEEFRFGIKAAE-EQLSARGMDASLSHQSLVALSEKLA
          LQED.KKAELHLSTERAKVDNR.Q.MDFLK.KS.EFRFGIKAAE.EQLSARGMDASLSHQSLVALSEKLA
Retrocopy LQEDLKKAELHLSTERAKVDNRHQSMDFLKPKSVEFRFGIKAAE>EQLSARGMDASLSHQSLVALSEKLA

Parental  RLKQQTIPLKKKLESYLDLMPNPS-LAQVKIEEAKRELDSIEAELTRRVDMMEL
          .LKQQTIPLKKKLES.LDLMPNPS.LAQVKIEEA.RELDSIEAELTRRVDMMEL
Retrocopy KLKQQTIPLKKKLES*LDLMPNPS<LAQVKIEEAERELDSIEAELTRRVDMMEL

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	1.88 RPM
SRP007412_cerebellum	0.00 RPM	3.94 RPM
SRP007412_heart	0.00 RPM	1.92 RPM
SRP007412_kidney	0.00 RPM	5.31 RPM
SRP007412_liver	0.00 RPM	3.90 RPM
SRP007412_testis	0.11 RPM	9.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3092 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001139	3 retrocopies	retro_chof_237, retro_chof_2496, retro_chof_255,
Homo sapiens	ENSG00000152240	3 retrocopies	retro_hsap_3247, retro_hsap_4075, retro_hsap_4655,
Gorilla gorilla	ENSGGOG00000010098	2 retrocopies	retro_ggor_2210, retro_ggor_2888,
Loxodonta africana	ENSLAFG00000010897	1 retrocopy	retro_lafr_1063,
Macaca mulatta	ENSMMUG00000003124	2 retrocopies	retro_mmul_2043, retro_mmul_2476,
Monodelphis domestica	ENSMODG00000003208	1 retrocopy	retro_mdom_743,
Nomascus leucogenys	ENSNLEG00000011216	3 retrocopies	retro_nleu_1091, retro_nleu_1698, retro_nleu_2043,
Pongo abelii	ENSPPYG00000009131	3 retrocopies	retro_pabe_2693, retro_pabe_3344, retro_pabe_3615,
Pan troglodytes	ENSPTRG00000009992	3 retrocopies	retro_ptro_2195, retro_ptro_2762, retro_ptro_3092 ,
Tupaia belangeri	ENSTBEG00000010911	4 retrocopies	retro_tbel_1209, retro_tbel_1348, retro_tbel_3868, retro_tbel_4672,