RetrogeneDB ID: retro_cpor_862

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:57514166..57514589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSCPOG00000003638
• Aliases: None
• Description: Synaptosomal-associated protein [Source:UniProtKB/TrEMBL;Acc:H0V1C5]

Sequence

>retro_cpor_862
GAGAGACAGAGAAAACTAACAGAACTCAACAAGTGCTACAGCTTTTGTGTCTGTCTATGTAACAGGACAAAGAACTTTGA
GTCTGGCAAGACCTATAAAGCAACATGGTGAGATGGAGAGGCAGTGCACCTTGGAACTTGGTATCAAAGCAACCAGCAGA
GTGAGTAGTAAACAGCCAACCCCACAAGCAAGGGAGCAGCCCATAGGAGGTACGTTAAAGGTACAACTAATGACACCAGA
GAAGATGAGATGGAAGAGAAGCTGACTCAAGTGAAAAATAGCTTGCGAAATCTCAAGAACGTGGCTTGGGGTATGGGCAG
TGAAACTAAAGCTCAAAATCAACAAATAAACTGGATCATAGAAAAGGCTGACACCAACAACTATCATATTGACATTTCCA
ATACCAGGGCAAAGAAACCCATT

Alignment

ORF - retro_cpor_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.62 %
• Parental protein coverage: 67.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETEKTLTELNKCCGLCVCPCNRTKNFESGKAYKAAWGEGG-GNSPSNVVSKQPA-RVTNGQPQQPATGAV
          E....LTELNKC...CVC.CNRTKNFESGK.YKA.W..G..G..P.N.VSKQPA.RV...QP...A....
Retrocopy ERQRKLTELNKCYSFCVCLCNRTKNFESGKTYKATW*DGE<GSAPWNLVSKQPA<RVSSKQPTPQAREQP

Parental  SGG-YIKRITNDAKEEEMEENLTQVGNILGNLKNLALDMGNEIDAQNRQIDSITKKVEANKDRIDIANTR
          .GG.Y.K..TND..E.EMEE.LTQV.N.L.NLKN.A..MG.E..AQN.QI..I..K...N...IDI.NTR
Retrocopy IGG<YVKGTTNDTREDEMEEKLTQVKNSLRNLKNVAWGMGSETKAQNQQINWIIEKADTNNYHIDISNTR

Parental  AKKLI
          AKK.I
Retrocopy AKKPI

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
SRP017611_brain	0.00 RPM	6.61 RPM
SRP017611_kidney	0.00 RPM	18.53 RPM
SRP017611_liver	0.00 RPM	16.98 RPM
SRP040447_lung	0.00 RPM	31.65 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.36 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_862 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_862 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862 ,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,