RetrogeneDB ID: retro_ggor_2398

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:6489805..6490086(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAPC5
• Ensembl ID: ENSGGOG00000003693
• Aliases: None
• Description: None

Sequence

>retro_ggor_2398
CAGGAACTGCGCGAGGAGGAGGAGACACTGCTCCTGTCGAAGGCAGCCCCCGCATGACCTGCTGAATCACATCAAGGTTG
AAGCACTGGCCCTCCAATCAACGATTAGTTCTAGGAGAGGGGATGAGGTGCTGTCTCCTCCAACTTCTCCAACTGTGCCT
GAACAGTCACACGTCATGTCAGTGCATATAGACAATGAAGCATCAGTCAACCAAACTACGCTGGAGTGGAGCATAGAGTC
CTGTGACAGAAGAAGAGGAGGAAGAGAAAGAAGAATCAGAT

Alignment

ORF - retro_ggor_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QELRKEEETLLRLKAAL-HDLLNRLKVEELALQSMISSRRGDEMLS---SHTVPEQSHDMLVHVDNEASI
          QELR.EEETLL..KAA..HDLLN..KVE.LALQS.ISSRRGDE.LS...S.TVPEQSH.M.VH.DNEAS.
Retrocopy QELREEEETLLLSKAAP>HDLLNHIKVEALALQSTISSRRGDEVLSPPTSPTVPEQSHVMSVHIDNEASV

Parental  NQTTLELSTKS-HVTEEEEEEEEEE
          NQTTLE.S..S....EEEEE.EE..
Retrocopy NQTTLEWSIES>VTEEEEEEKEESD

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	2.59 RPM	15.25 RPM
SRP007412_cerebellum	0.00 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	5.66 RPM
SRP007412_kidney	0.12 RPM	8.95 RPM
SRP007412_liver	0.00 RPM	3.51 RPM
SRP007412_testis	0.10 RPM	15.85 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_2398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2398 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1815

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398 ,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,