RetrogeneDB ID: retro_ggor_2888

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:18880641..18881140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS1
• Ensembl ID: ENSGGOG00000010098
• Aliases: None
• Description: None

Sequence

>retro_ggor_2888
ACTAGTTTTATCCCTGTAGTGAATGATTTGACCTCTTACCTCTTTCGTACCAAATCCAAAAGTGAAGAAATCAAGATTGA
ACTGGAAAAATTTGAAAAAAAATCTAACTGCAACTTTAGTATTAGAAAAATGTCTACAAGAGGATCTCAAGAAAGCAGAG
TTGCATCTGTCTACAGAAAGGGCCAAAGTTGATAATCGTCATCAGAACATGGACTTTCTAAAACCAAAGTCAGTGGAATT
CAGATTTGGAATCAAGGCTGCAGAGGGAGCAACTTTCAGCCAGAGGCATGGATGCTTCTCTGTCTCATCAGTCCCTAGTA
GCACTGTCAGAGAAAATGGCAAAATTAAAACAACAGACTATACCTTTGAAGAAAAAATTGGAGTCCTAGTTAGATTTAAT
GCCGAATCCATCCTTGCTCAAGTGAAAATTGAAGAAGCAGAGCGAGAATTAGATAGCATTGAAGCTGAACTTACAAGAAG
AGTAGACATGATGGAACTG

Alignment

ORF - retro_ggor_2888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 72.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEFIPAVNDLTSDLFRTKSKSEEI-KIELEKLEKNLTATLVLEKCLQEDVKKAELHLSTERAKADNRRQN
          ..FIP.VNDLTS.LFRTKSKSEEI...........LTATLVLEKCLQED.KKAELHLSTERAK.DNR.QN
Retrocopy TSFIPVVNDLTSYLFRTKSKSEEI>RLNWXXXXXXLTATLVLEKCLQEDLKKAELHLSTERAKVDNRHQN

Parental  MDFLKAKSEEFRFGIKAAE-EQLSARGMDASLSHQSLVALSEKLARLKQQTIPLKKKLESYLDLMPNPS-
          MDFLK.KS.EFRFGIKAAE.EQLSARGMDASLSHQSLVALSEK.A.LKQQTIPLKKKLES.LDLMPNPS.
Retrocopy MDFLKPKSVEFRFGIKAAE>EQLSARGMDASLSHQSLVALSEKMAKLKQQTIPLKKKLES*LDLMPNPS<

Parental  LAQVKIEEAKRELDSIEAELTRRVDMMEL
          LAQVKIEEA.RELDSIEAELTRRVDMMEL
Retrocopy 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	1.58 RPM
SRP007412_cerebellum	0.00 RPM	2.60 RPM
SRP007412_heart	0.00 RPM	1.53 RPM
SRP007412_kidney	0.00 RPM	4.21 RPM
SRP007412_liver	0.00 RPM	2.98 RPM
SRP007412_testis	0.00 RPM	18.96 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2888 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4655

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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,