RetrogeneDB ID: retro_cpor_1505

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:51272161..51272462(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSCPOG00000011075
• Aliases: None
• Description: Stathmin [Source:UniProtKB/TrEMBL;Acc:H0VID0]

Sequence

>retro_cpor_1505
CTGGGGGAAATTCAGAAGAAACTGGAAGCTGCAAATGAAAGATGCAAGTTCTATAAAACTGAAGTCCTAAAGCAGCTTGA
TAAGAAAAAAGAGCATGAAAAAGAAGTGGTTCAAAAGCAGCAGTAGAAGAGGCAACAACTTCAGTAAACTGGCAGGAGAG
AAATCAACCCACAAAACGGAAACTAACAGAGAAATCCAAGAGACACAAATGGCTGCCATACTGGACTGTTTGGGAGAGGA
TAAACATACTGAAGAAGTAGAAAAGAACCAAGAATCCAAAGATCCTGCTGATGATACTGAA

Alignment

ORF - retro_cpor_1505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 67.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEEIQKKLEAAEERRKSHEAEVLKQLAEKREHEKEVLQK-AIEENNNFSKMAEEKLTHKMEANKENREAQ
          L.EIQKKLEAA.ER.K....EVLKQL..K.EHEKEV.QK......NNFSK.A.EK.THK.E.N.E..E.Q
Retrocopy LGEIQKKLEAANERCKFYKTEVLKQLDKKKEHEKEVVQK>SSRRGNNFSKLAGEKSTHKTETNREIQETQ

Parental  MAAKLERLREKDKHIEEVRKNKESKDPADETE
          MAA.L..L.E.DKH.EEV.KN.ESKDPAD.TE
Retrocopy MAAILDCLGE-DKHTEEVEKNQESKDPADDTE

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	242.14 RPM
SRP017611_kidney	0.00 RPM	20.83 RPM
SRP017611_liver	0.00 RPM	7.92 RPM
SRP040447_lung	0.00 RPM	19.80 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1505 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1505 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505 ,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,