RetrogeneDB ID: retro_ggor_1714

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:17036733..17038313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGAP42
• Ensembl ID: ENSGGOG00000011397
• Aliases: None
• Description: None

Sequence

>retro_ggor_1714
CAAGTAGTTGAAAGCCATGGGATCATCACATTACAGGCCTTCTCAGACGCTAATAGGAAACTCTGGCTTGAAGCCACGGA
TGGGAAGGAAACGATTTATACTCTGCCTGACATTATAAGCAAGAAAGAAGAAAGGTATTTGAATGAAGCAGGGTTCAATT
TTGTGAGAAACTGCATTCAAGCTGTGGAAACAAGCGGTATCACCATTTTAGGCCTCTACTGAATAGGAGGAGTGAACCCC
AAAGTTCAAAAACTTGTGAATATCATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGAC
AATGAGTGGGCTGAAAAACCACCTCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATT
GCTGTTAAATCTGATGACCAAAACTACAGGGTGGAGGCTGTACATGCATTGGTGTGCAAATTGCCAGAGAAAAACAGAGA
GATGCTGGACATCTTAATAAAACATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTGTCTCAAATCTTG
GTGTCATATTTGGCCCAACTCTAATGAGAGCACAAGAATAAGCTGTAGCTGCTATGGTGAATATTAAATTTCAGAATATT
GTGTTAGAAATTCTTACAGAGCACAATGAAACGATTTTTCATACTGCTCCAGACCCAAGCACTCCTCTTCCTCAGCCTCA
GTCTCGATCTGGATCCCAAAAGACACAAGCAATCTGCCTCTCTACAGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCAT
GCCTGGCTGAACCTGATAGTGACTCCTATAGCAGCAGCCCAGACAGCACCCCCATGGGGAACAACAAGTCACTCTCTTCT
CTTTCCTCAGAACAAAATAGCACTACAAAGTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGC
AACCCCGTCATCTTCCCATGGACAGAAAAGCCTTGGTCTCTGGACAACCAGTCCTGAATCAATTTCTAGAGAAGATGCAA
CAAAGACAGATGCAGAATCAGATTGCCAGAGTGTTGCTTCGGTCACTAGCCCAGGGGATGTTTCCCCACCCATAGACCTA
GTCAAGAAAGGGCCTTATGGGCTTTCAGAACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGG
AAACACCAGCTACAGTGGATCTATTCAAAGCTTAACTTCTGTAGGTTCCAAGAAGACACCCAAAGCTTCAAACCCAGACC
TGCCTCCAAAAATGTGCAGGAGATTAAGACTAGACACCGCCTAAAGCAATGGCTATCAGCGTCCTGGCTCAGTAGTGGCA
GCAAAAGCTCAACTGTTTGAAAATGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTG
TAAAGCAGAGCACAGCGTGAGTTTTCCTTCCCACAAGGAGTGATATTTTCCAGCGTGGCCCATCAGTGGAACCAGGATGG
TTAAAGGCAACTTATGAAGGCAAAACGGGACTAGTTCCAGAAAATTATGTTGTCTTCCTC

Alignment

ORF - retro_ggor_1714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 60.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAGFNFVRKCIQAVETRGITIL
          .VVE.HGIITLQAFS.ANRKLWLEA.DGKE.IYTLP.IISKKEE.YLNEAGFNFVR.CIQAVET.GITIL
Retrocopy QVVESHGIITLQAFSDANRKLWLEATDGKETIYTLPDIISKKEERYLNEAGFNFVRNCIQAVETSGITIL

Parental  GLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCLAEPLMTYKLHKDF-IIAVK
          GLY.IGGVN.KVQKL.N..FSPKSPPDIDI..ELWDNKT..SGLKN.LRC.A.PLMTYKLHKD..IIAVK
Retrocopy GLY*IGGVNPKVQKLVNIIFSPKSPPDIDI--ELWDNKTM-SGLKNHLRCFAAPLMTYKLHKDL>IIAVK

Parental  SDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLGVIFGPTLMRAQEETVAAMM
          SDDQNYRVEAVHALV.KLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLGVIFGPTLMRAQE..VAAM.
Retrocopy SDDQNYRVEAVHALVCKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLGVIFGPTLMRAQE*AVAAMV

Parental  NIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTGSRKPRGRYTPCLAEPDSDSY
          NIKFQNIV.EIL.EH.E.IFHTAPDPS.PLPQPQSRSGS..T.AICLSTGSRKPRG..TPCLAEPDSDSY
Retrocopy NIKFQNIVLEILTEHNETIFHTAPDPSTPLPQPQSRSGSQKTQAICLSTGSRKPRGTCTPCLAEPDSDSY

Parental  SSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSNGQKSLGLWTTSPESSSREDA
          SSSPDSTPMG...SLSS.SSEQNSTTKSASCQPREKSGGIPWIATPSSS.GQKSLGLWTTSPES.SREDA
Retrocopy SSSPDSTPMGNNKSLSSLSSEQNSTTKSASCQPREKSGGIPWIATPSSSHGQKSLGLWTTSPESISREDA

Parental  TKTDAESDCQSVASVTSPGDVSPPIDLVKKEPYGLSGLKRASASSLRSISAAEGNKSYSGSIQSLTSVGS
          TKTDAESDCQSVASVTSPGDVSPPIDLVKK.PYGLS.LKRASASSLRSISAAEGN.SYSGSIQSLTSVGS
Retrocopy TKTDAESDCQSVASVTSPGDVSPPIDLVKKGPYGLSELKRASASSLRSISAAEGNTSYSGSIQSLTSVGS

Parental  KETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSPKPVSSGRQAKAMYSCKAEHS
          K.TPKAS.NPDLPPKMCRRLRLDTA.SNGYQRPGSVVAAKAQLFENVGSPKPVSSG.QAKAMYSCKAEHS
Retrocopy KKTPKAS-NPDLPPKMCRRLRLDTA*SNGYQRPGSVVAAKAQLFENVGSPKPVSSGHQAKAMYSCKAEHS

Parental  -HELSFPQGAIFSNVY-PSVEPGWLKATYEGKTGLVPENYVVFL
          ..E.SFPQG.IFS.V..PSVEPGWLKATYEGKTGLVPENYVVFL
Retrocopy <REFSFPQGVIFSSVA<PSVEPGWLKATYEGKTGLVPENYVVFL

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	5.75 RPM
SRP007412_cerebellum	0.00 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	1.06 RPM
SRP007412_kidney	0.00 RPM	14.72 RPM
SRP007412_liver	0.00 RPM	7.31 RPM
SRP007412_testis	0.00 RPM	13.47 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_1714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1714 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005829	1 retrocopy	retro_ecab_997,
Homo sapiens	ENSG00000165895	2 retrocopies	retro_hsap_2156, retro_hsap_2318,
Gorilla gorilla	ENSGGOG00000011397	2 retrocopies	retro_ggor_1714 , retro_ggor_1758,
Pongo abelii	ENSPPYG00000003799	1 retrocopy	retro_pabe_2095,
Pan troglodytes	ENSPTRG00000004204	4 retrocopies	retro_ptro_1641, retro_ptro_1692, retro_ptro_3083, retro_ptro_892,