RetrogeneDB ID: retro_cjac_1958

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:130853102..130853435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP7
• Ensembl ID: ENSCJAG00000016289
• Aliases: None
• Description: vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486]

Sequence

>retro_cjac_1958
TTCCTGGAGGTGACAGAGCATATTCTGGCTAAGATACCTTCTGAAAATAACAAACTAAGGTACTCACATGGCAATTATTT
GTTTCATTACATCTGCCAAGACAGGATTGTATATCTTTGTATCACGGATGATGATTTTGAATGTTCCCGAGACTTTAATT
TTCTGAATGAGATAAAGAAGAGGTTCCAGACTGCTTATGGTTCAAGAGCACGGACAGCACTTCCATATGCCAAGGAAAGT
GAGTTCTCAAGTGTCTTGGCTGCACAGCTGAAGCATCACTCTGAGAATAAGGGCCTAGACAAAGTGATGGAGACTCAACC
CCAAGTGGATGAA

Alignment

ORF - retro_cjac_1958 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 77.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFNFLNEIKKRFQTTYGSRA
          FLEVTE.ILAKIPSENNKL.YSHGNYLFHYICQDRIVYLCITDDDFE.SR.FNFLNEIKKRFQT.YGSRA
Retrocopy FLEVTEHILAKIPSENNKLRYSHGNYLFHYICQDRIVYLCITDDDFECSRDFNFLNEIKKRFQTAYGSRA

Parental  QTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDE
          .TALPYA..SEFSSVLAAQLKHHSENKGLDKVMETQ.QVDE
Retrocopy RTALPYAKESEFSSVLAAQLKHHSENKGLDKVMETQPQVDE

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
SRP051959_colon	0.02 RPM	18.33 RPM
SRP051959_heart	0.00 RPM	18.22 RPM
SRP051959_kidney	0.00 RPM	33.10 RPM
SRP051959_liver	0.00 RPM	23.87 RPM
SRP051959_lung	0.00 RPM	23.86 RPM
SRP051959_lymph_node	0.00 RPM	17.67 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.87 RPM
SRP051959_spleen	0.00 RPM	26.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1958 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1958 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016289	2 retrocopies	retro_cjac_1958 , retro_cjac_2410,
Cavia porcellus	ENSCPOG00000024405	1 retrocopy	retro_cpor_714,
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720,