RetrogeneDB ID: retro_cpor_805

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:12515977..12516542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC30A9
• Ensembl ID: ENSCPOG00000000374
• Aliases: None
• Description: None

Sequence

>retro_cpor_805
GCCACCACCACTGCAGCCCACAGGCACGCTGGTCTTTTCTGCATCGGCTCCTCTCGAGCTGCAGGAGTGGCCCACCTCTC
CAGCGACCATCAAGAATGCCAGAATTTAGTGACATTTGATAATACACATATATTGTTCCTTATAGTGGTTCACATATTTG
TACACCAAGTCAAGAAAAGCTGCACTCTATAAATACTCAGAAAGAAGGACACGGATCACAAACTCTCCGAGTGGGAAAAG
AAGAGCCATCATGTGATGAACGAGCAAAAAACATAGGTGCAGAACTCAAAAGCTCTACTGAAGCAAGAACCTCTCCAAAT
AAGTCAAAGCAGCTCCTAAGCAAGGGGAAAAGGCTCAAAGTACATTCAGAAAAATTTCCTTGCTGGAGTCAGAACAATCT
ATAAGTTTTGCCTTAAGTCTAGTAATCCAGAACAACTTGGAAAAATCAGGTAACAAAGTCCCTGTGAACATACTGAGTCC
TTTATTAAATACTTGAGATCAGATGGGGACCAAAAATCTTTGGACATTTAGGGAGAGCTTTGAAGCTTTTGCTAGAGAAA
TGAAA

Alignment

ORF - retro_cpor_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 87.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AAATTAHRCSWSFLCRLRLSCRAACRGSSDRRVEWQNLVTFGN-FACMVPYRHPHICTLSQIKLYSTNIQ
          A..T.AHR....F.C............SSD...E.QNLVTF.N.....VPY...HICT.SQ.KL.S.N.Q
Retrocopy ATTTAAHRHAGLF-CIGSSRAAGVAHLSSDHQ-ECQNLVTFDN<YTYIVPYSGSHICTPSQEKLHSINTQ

Parental  KEGQGSQTHRVEKV-PSFGETAENIGAELKAPLK-QEPLQVRVKAVLKKREY-GSKYTQNNFITGVRAIN
          KEG.GSQT.RV.K..PS..E.A.NIGAELK........L...VKA..K..E..GSKY.Q.NF..GVR.I.
Retrocopy KEGHGSQTLRVGKEEPSCDERAKNIGAELKSSTE<SKNLSK*VKAAPKQGEK<GSKYIQKNFLAGVRTIY

Parental  EFCLKSSDLEQLRKIRRRSPHEDTESFTVYLRSDVEAKSLEVWG-SPEALAREKK
          .FCLKSS..EQL.KIR..SP.E.TESF..YLRSD...KSL...G.S.EA.ARE.K
Retrocopy KFCLKSSNPEQLGKIR*QSPCEHTESFIKYLRSDGDQKSLDI*G>SFEAFAREMK

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	0.06 RPM	20.59 RPM
SRP017611_kidney	0.00 RPM	15.49 RPM
SRP017611_liver	0.00 RPM	8.23 RPM
SRP040447_lung	0.00 RPM	4.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_805 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_805 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805 ,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658,