RetrogeneDB ID: retro_cpor_1442

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_84:4731686..4732160(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP29
• Ensembl ID: ENSCPOG00000003137
• Aliases: None
• Description: None

Sequence

>retro_cpor_1442
ACAGAGAATATGACAGACAAGATGAATCAGGACTTGAAGACCACCCTGAGGGACATCAACGGCATGAAAGAGTGTGTTCA
GTGAGTTCGGCAATTACTTCAAATCCAAACCAGTAGAGACCCCAGCTGAACAGAATGGCACATCCATCCCTCAGCCTAAC
AGCAGATTGAAAGAAGCAACACGTGCAAGTGAAGAACCAGAGGAAAAGTTCCAGGCCAACCACCCAAAACTCAGCAAGCC
GGATGTTGTAGACCCCCAGACTGGCTCTGCTGTGAGTACTGAGGTTTACCCAAAAACCTGCTCCTTCTGGCCTATCACCA
GAAGACTGACAACAGTCTAGGTGAACTATACATGGCACTGAGCCAACTGAAGGACATAGCTTTGGGGATGCAGACGACAA
CTGAGGAGCAAGATGATATTCTTGAACAGCTGACAACCAGAGTGGATGAGTTAGATATCAAAATAAAAAGCACA

Alignment

ORF - retro_cpor_1442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 62.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEKMVDKMDQDLKTSQRHINSIK-SVFGGLVNYFKSKPVETPTEQNGTLTPQTNSRLKEAISISKEQEEK
          TE.M.DKM.QDLKT..R.IN..K.SVF....NYFKSKPVETP.EQNGT..PQ.NSRLKEA...S.E.EEK
Retrocopy TENMTDKMNQDLKTTLRDINGMK>SVFSEFGNYFKSKPVETPAEQNGTSIPQPNSRLKEATRASEEPEEK

Parental  YQASHPNLRKLDDVDSDSQTSSSVNTEAYPK-NPHLRAYHQKIDSNLDELSMGLGRLKDIALGMQTEIEE
          .QA.HP.L.K.D.VD...QT.S.V.TE.YPK.N..L.AYHQK.D..L.EL.M.L..LKDIALGMQT..EE
Retrocopy FQANHPKLSKPDVVDP--QTGSAVSTEVYPK<NLLLLAYHQKTDNSLGELYMALSQLKDIALGMQTTTEE

Parental  QDDILDRLTTKVDKLDINIKST
          QDDIL..LTT.VD.LDI.IKST
Retrocopy QDDILEQLTTRVDELDIKIKST

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	5.46 RPM
SRP017611_kidney	0.00 RPM	14.03 RPM
SRP017611_liver	0.00 RPM	5.05 RPM
SRP040447_lung	0.00 RPM	7.52 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1442 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1442 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015201	1 retrocopy	retro_cfam_1542,
Cavia porcellus	ENSCPOG00000003137	1 retrocopy	retro_cpor_1442 ,
Dasypus novemcinctus	ENSDNOG00000005913	4 retrocopies	retro_dnov_1401, retro_dnov_1855, retro_dnov_2001, retro_dnov_2364,
Nomascus leucogenys	ENSNLEG00000000108	1 retrocopy	retro_nleu_2645,
Otolemur garnettii	ENSOGAG00000013003	1 retrocopy	retro_ogar_3493,