RetrogeneDB ID: retro_ggor_2187

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:80809312..80809933(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC3
• Ensembl ID: ENSGGOG00000013490
• Aliases: None
• Description: None

Sequence

>retro_ggor_2187
GTGGTGCTGGTCCCCACCCACCACTTCAGAGACTTTGAGAGGAAACCAGAGTACCCATAGCTGGAGATGCCTGTCCGACC
TCCCTACCCTGGTCCTATGAGAACCATGTGGCTTATCCACGATGGCTGTGGCATTGCCTATGCGATCATCACCTGGTTTC
TGGTCCTCTATGCGGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCCGAGACTATGCATAGAGCACCATCAGTGGA
ATTGTGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGACACCGGAGCAGTGCCCAA
ATGAAATGCCACAAATAATTCATCCAGAGTTTACAGATGAAGCCCAGGCATGTGGTATACTCGTGTCCCAGTGCTGTAGC
CTCAAGCCTGACCGAGCCTGCCGCTGCAGTGTTTGTAAGGGGTGCATTCGCAGGGTGGACCCCCACTGTCCCTGGGTCAA
CATCTGCATCGAAGAGAACAACCAGAAGTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTGCCTGCCCTCA
TCATGGTGGATTACACTTCCTGGATTGTTGTGAAGAAAATTGCTCAAATCTCCCGAAGCCT

Alignment

ORF - retro_ggor_2187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.5 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMLIPTHHFRDIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
          ..L.PTHHFRD.ERKPEY...E..V.PPYPGP..TMW.I.DGCGIA.AI.TWFLVLYAEFVVLF.MLIPS
Retrocopy VVLVPTHHFRDFERKPEYP*LEMPVRPPYPGPMRTMWLIHDGCGIAYAIITWFLVLYAEFVVLFFMLIPS

Parental  RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNAT-KEFIESLQLKPGQVVYKCP-KCCSIKPD
          RDY..S.I.GIVFNLL.FLALASHC.AMLTD.GAVPK.NAT.K.FI.SLQ.KP..VVY.CP..CCS.KPD
Retrocopy RDYA*STISGIVFNLLTFLALASHCQAMLTDTGAVPK*NAT<K*FIQSLQMKPRHVVYSCP<QCCSLKPD

Parental  RAHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEEDWTKCSS
          RA..CSVCK.CIR..D.HCPWVN.C..ENNQK.FVLF.M..ALISL.ALIMV.G.HFL.C.EE....CS.
Retrocopy RACRCSVCKGCIRRVDPHCPWVNICIEENNQKCFVLFIMCTALISLPALIMV<GLHFLDCCEEN---CSN

Parental  FSPP
          ...P
Retrocopy LPKP

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	27.67 RPM
SRP007412_cerebellum	0.00 RPM	24.35 RPM
SRP007412_heart	0.00 RPM	9.66 RPM
SRP007412_kidney	0.00 RPM	42.73 RPM
SRP007412_liver	0.00 RPM	19.84 RPM
SRP007412_testis	0.00 RPM	113.13 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_2187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2187 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3221
Pan troglodytes	retro_ptro_2171
Pongo abelii	retro_pabe_2668

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Gorilla gorilla	ENSGGOG00000013490	1 retrocopy	retro_ggor_2187 ,
Loxodonta africana	ENSLAFG00000012733	1 retrocopy	retro_lafr_136,
Nomascus leucogenys	ENSNLEG00000006024	1 retrocopy	retro_nleu_2725,
Rattus norvegicus	ENSRNOG00000004344	1 retrocopy	retro_rnor_1688,