RetrogeneDB ID: retro_cpor_364

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_132:1978174..1978580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSCPOG00000000031
• Aliases: None
• Description: None

Sequence

>retro_cpor_364
ATAAATGACTTTGAAAGAGAGAAAAATCTTCTTTGGGTATTTCTGATTCGAAGGGGTCTATGTGTGCAGTGTCTGGCAAT
GTGGAGACTGATGAAAGTGTCCTCATGAGAAGATAGAAGCACAGAAGGCAGAACTCCAGGAAGAATGCCATCGCCTATGA
TTGCTATATTAAAGAAGTCCTCAGACACCAACCTGGCATCTTCCCCAAGACCTCCAACAAATTTAAGAAGTACAGTTGGT
GGTCTGGGACCTGCAGATCAAGCTCTGGAAGATGGTGCTGCATTTTTGGGACCCTCTGACTGAAGAAAGATGCAATTTGC
AAAAAATACACCCTGTGGACCCAGGGGAAATGGAAATTGAATCCATAGAAAGCAGCTCCAAGTCCCAGGTGAGCTCATGG
GATAAC

Alignment

ORF - retro_cpor_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INDFGRER-KSSSGSSDSKESTCAVPADVETDESVLMRR--QKQINYGKNTIAYDRYIKEVPRHLRQPGI
          INDF.RE..KSS.G.SDSK.S.CAV...VETDESVLMRR......N..KN.IAYD.YIKEV.RH..QPGI
Retrocopy INDFEREK<KSSLGISDSKGSMCAVSGNVETDESVLMRR*KHRRQNSRKNAIAYDCYIKEVLRH--QPGI

Parental  HPKTPNKFKKYSRRS-WDQQIKLWKVALHFWDPPAEEGCDLQEIHPVDLGEMETEFIESSSESQASSQDN
          .PKT.NKFKKYS..S.WD.QIKLWK..LHFWDP..EE.C.LQ.IHPVD.GEME.E.IESSS.SQ.SS.DN
Retrocopy FPKTSNKFKKYSWWS<WDLQIKLWKMVLHFWDPLTEERCNLQKIHPVDPGEMEIESIESSSKSQVSSWDN

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	17.25 RPM
SRP017611_kidney	0.10 RPM	15.70 RPM
SRP017611_liver	0.00 RPM	13.28 RPM
SRP040447_lung	0.00 RPM	23.08 RPM
SRP040447_skeletal_muscle	0.01 RPM	6.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_364 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_364 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364 ,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,