RetrogeneDB ID: retro_ggor_1077

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:1443494..1444205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSGGOG00000010695
• Aliases: None
• Description: None

Sequence

>retro_ggor_1077
CTCATGAAAGACCAGCATTTATGAGATTCCTTCTCAGATTTCACATCATTCAATATTTTGATGGATATGTTATTTATCAA
AGGCAAATATAAAAGTGCTTTGGAAGTATTGATAGAGATGAAAAATCAAGGTGTGAAATTCACCAAAGATCCTATGTTCT
TAGTTTTGCAGTTTGCAACAAACTGAATAGCCCTGAGTCTTTCAAAATCTGTTCTACATTAAGAGAAGAAGCCCCACTCA
AAGGAGAGGTTCTCTCCAGCAGAGTATCCCGTTTCTTTGTGGCGTTAGCTCTGAATCAGAACCAAGTGGCAAAAGCTATG
TCCATTTTTTTCTCAAACCATGAATCCAGAAAGCATAGCCTGCACTTACTTAACTATTATAATCCATATCCAGTCAAATA
TGTTGGAAACCCTGATAGAGACACTAAAAAAATGCTGCAGAAGGAAATTTATTAAAATTTGTGAAAAGACATGCATTCTC
AGAGGAAGTGCTGGAAAAAGTGAAGGAAAAGTGAGGGATATGCCTGCCCCTGTGGCCAGATTTAATGAGATCTATGGAAA
ACTGCACATCAGTGGCCAGGTCACCGCTTGTACTTTGGGTACTCTGCTCTGCCACACCCCCAGGGACAGGAAATCCCATA
TGTTGCTATTAAACAAGAGGATGATGAGCCATTGGACCTTCCAGTCACTCAACCGGTCCTTTTTGGCTGAG

Alignment

ORF - retro_ggor_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.59 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALQVLIEMKNQDVKFTKD-TYVLAFAICYKLNSPESFK
          LMKDQHL...FSD.TSFNILMDMLFIKGKYKSAL.VLIEMKNQ.VKFTKD..YVL.FA.C.KLNSPESFK
Retrocopy LMKDQHL*DSFSDFTSFNILMDMLFIKGKYKSALEVLIEMKNQGVKFTKD<SYVLSFAVCNKLNSPESFK

Parental  ICTTLREEALLKGEILSRRASCFAVALALNQNEMAKAMSIF-SQIMNPESIACINLNIIIHIQSNMLENL
          IC.TLREEA.LKGE.LS.R.S.F.VALALNQN..AKAMSIF.SQ.MNPESIAC..L.IIIHIQSNMLE.L
Retrocopy ICSTLREEAPLKGEVLSSRVSRFFVALALNQNQVAKAMSIF>SQTMNPESIACTYLTIIIHIQSNMLETL

Parental  IKTL-KNAAEGNLSKFVKRHVFSEEVLAKVRE-KVKDVPALVAKFDEIYGTLHITGQVTTDSLDAVLCHT
          I.TL.KNAAEGNL.KFVKRH.FSEEVL.KV.E.KV.D.PA.VA.F.EIYG.LHI.GQVT...L...LCHT
Retrocopy IETL>KNAAEGNLLKFVKRHAFSEEVLEKVKE<KVRDMPAPVARFNEIYGKLHISGQVTACTLGTLLCHT

Parental  PRDRKSHTLLLNKRMVSRRTFQPLSQSLLAE
          PRDRKSH.LLLNKRM.S..TFQ.L..S.LAE
Retrocopy PRDRKSHMLLLNKRMMSHWTFQSLNRSFLAE

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	12.66 RPM
SRP007412_cerebellum	0.00 RPM	8.04 RPM
SRP007412_heart	0.00 RPM	4.75 RPM
SRP007412_kidney	0.00 RPM	11.74 RPM
SRP007412_liver	0.00 RPM	7.17 RPM
SRP007412_testis	0.00 RPM	14.71 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_1077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1077 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077 , retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,