RetrogeneDB ID: retro_cpor_994

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:752531..753594(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSCPOG00000008524
• Aliases: None
• Description: None

Sequence

>retro_cpor_994
AAGAAAAAGCCAGAGGTGTTTAACTTTTCAGCAATTCACTTGATCCATGACCCCCAAGATTTTGCAGAAAAACTACTCAA
GCAGCTAGAGAACTCTAAGGAGAGGTTTGAAGTGAAGATGATGCTTATGAACCTCATCTCCAGATTGGTGGGAATCCATG
AGCTTTTTCTCTTCAATTTCTACCCCTTTCTCCAAAGCTTTCTGCAGCCCCACCAGAGAGAAGTAACAAAGATCCTCCTG
TTTGCTGCACAAACATCTCATCATTTTTTACCTCCAAAGATCATTCAGTCATTGCTTATGACTGTGGCCAACAATTTTGT
TACTGACAAGAACTCTAGGGAGGTCATGACAGTAGGTATCAACGCTATAAAGGAGATAACAGCTCAATGTCCTCTAGCCA
TGACTGAGGAGCTTCTCCAAGACCTGGCTCAATATAAGACCCACAAAGATAAGAATGTAATGATCTCTGCTAGAACTTTG
ATCCAGCTCTTCCGGACGCTGAATCCTCAGATGTTACAAAAAAAATTCCGGGGCAAACCTACAGAAGCTTCTGTAGAAGC
AAGAGTACAAGAATATGGTGAATTAGATGCTAAAGATTACGTTCCAGGAGCAGAGGTTCTGGAAATTGAGAAAGAAGAGG
ATGCTGAAAAATGATAAAGATGGGTGGGAAAGTACCAGTCTCAGTGAAGAGGAGGATGCTGATGGCGAATGGGTCAATGT
GCACCACTCTTCTGACGAAGAGCAGCAGCAAGAGATTTCCCGGAAACTAAGCAGCATGGACACGGAGAAGCAGAAGGCCT
AGGCTGCAGCTGTCAGCACCAGTCGAGTCTTGACTCAAGAGGACTTCCAGAAAATCCGCATGGCCCAAATGAGGAAAGAG
CTCGCTGCCGCCCCAGGGAAAGCCCAAAAGAGGAAATACATTGAAATAGACAGTGACGAGGAGCCCAGGGGTGAATTACT
GTCTCTTTGAGACATTGAACGTCTTCATAAAAAACCTAAGTCTGACAAGGAGACACGACTAGCAACTGCAATGGCTGGAA
AGACAGACCGAAAGGGATTTGTG

Alignment

ORF - retro_cpor_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 51.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKPEVFNFSAIHLIHDPQDFAEKLLRQLENSKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQRFLQP
          KKKPEVFNFSAIHLIHDPQDFAEKLL.QLENSKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQ.FLQP
Retrocopy KKKPEVFNFSAIHLIHDPQDFAEKLLKQLENSKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQSFLQP

Parental  HQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQ
          HQREVTKILLFAAQ.SHH..PP.IIQSLLMTVANNFVTDKNS.EVMTVGINAIKEITA.CPLAMTEELLQ
Retrocopy HQREVTKILLFAAQTSHHFLPPKIIQSLLMTVANNFVTDKNSREVMTVGINAIKEITAQCPLAMTEELLQ

Parental  DLAQYKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFRGKPTEASVEARVQEYGELDAKDYIPGAEVLEIE
          DLAQYKTHKDKNVM.SARTLIQLFRTLNPQML...FRGKPTEASVEARVQEYGELDAKDY.PGAEVLEIE
Retrocopy DLAQYKTHKDKNVMISARTLIQLFRTLNPQMLXXXFRGKPTEASVEARVQEYGELDAKDYVPGAEVLEIE

Parental  KEEDAE-NDEGDGWESTSLSEEEEADGEWVDVHHSSDEEQQQEISQKLSSMDTEERKAKAAAVSTSRVLT
          KEEDAE.ND..DGWESTSLSEEE.ADGEWV.VHHSSDEEQQQEIS.KLSSMDTE..KA.AAAVSTSRVLT
Retrocopy KEEDAE>NDK-DGWESTSLSEEEDADGEWVNVHHSSDEEQQQEISRKLSSMDTEKQKA*AAAVSTSRVLT

Parental  QEDFQKIRMAQMRKELAAAPGKAQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKT
          QEDFQKIRMAQMRKELAAAPGKAQKRKYIEIDSDEEPRGELLSL.DIERLHKKPKSDKETRLATAMAGKT
Retrocopy QEDFQKIRMAQMRKELAAAPGKAQKRKYIEIDSDEEPRGELLSL*DIERLHKKPKSDKETRLATAMAGKT

Parental  DRKEFV
          DRK.FV
Retrocopy DRKGFV

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	0.12 RPM	20.88 RPM
SRP017611_kidney	0.10 RPM	18.53 RPM
SRP017611_liver	0.09 RPM	13.23 RPM
SRP040447_lung	0.05 RPM	25.98 RPM
SRP040447_skeletal_muscle	0.01 RPM	9.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_994 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_994 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994 ,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,