RetrogeneDB ID: retro_cpor_693

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:2429347..2430150(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSCPOG00000014110
• Aliases: None
• Description: None

Sequence

>retro_cpor_693
TACAGGCAGAAGGCCCTCTCCTGCCACCCAGACAAAAACCCAGATAACCCCAAAGCAGCTGAACTCTTTCCACCAGCCTT
GGAAGTGTTGACTGATGCTGCAGCCAGGGCTGCATATGACAAGGTCAGAAAAGCCAAGAAGCAGGCAGTAGCGAGGACCC
AGAAACTTGATGAGTAAAGGAAAAGAGTGAAGCCTGACCTGGAGGCCCGGAGCAGCAGCCCCAGGCCCAGGGGAGTGAAG
AGGAGGAGGAGAACCGGAGCACCAGGACTCTGGAGCAGGAGATTGCACGCCTATGAGAAGACGGTTCCCGGCAGCTACAG
GATTAGCAGAGGCTCATCCAGGAGCAGATACGCCAGGACCGTGAGCAGAGGCTGACAGGAAAGGTGGAAAATAATGAAGG
CAAAGGAACTCCCAAACTGAAGCTAAACTGGAAGTGCAAAAAGGAAGATGAGTCCCAAGGTGGCTACTCCAAAGATGTCC
TCCTGCGGCTTTTACAGAAGTATGGTGAAGTTCTCAACCTGGTGATTTCCAGTAAAAAAGCAGGCACTGCCGTGGTGGAG
TTTGCGACTGTCAAGGCTGCGGAGCTGGCTTTCCGGAATGAAGTGGGCCTTGTGGATAACCCTCTGATTTCCTGGTTGGA
GGGACAGCCCCAGGGCACGGCAGGCCCCAGCCACCCAGAACTGTCAAAGGGCTCAGTGCTGTCAGAGAGGGACTACGAGA
GCCTTGTCATGATGCGCATGCGCCAGGCAGTCGAGCGCCAACAGCTGATCGCCTAGATGCAGCAGGAGGACAAGGGGCAG
CTC

Alignment

ORF - retro_cpor_693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YRQKALSCHPDKNPDNPKAAELFHQLSQALEVLTDAAARAAYDKVRKAKKQAAARTQKLDEKRKRVKLDL
          YRQKALSCHPDKNPDNPKAAELF.....ALEVLTDAAARAAYDKVRKAKKQA.ARTQKLDE.RKRVK.DL
Retrocopy YRQKALSCHPDKNPDNPKAAELF---PPALEVLTDAAARAAYDKVRKAKKQAVARTQKLDE*RKRVKPDL

Parental  EAR-ERQAQAQGSEEEEENRSTRTLEQEIARLREEGSRQLQEQQRLIQEQIRQDREQRLRGKVENNEGKG
          EAR.E.Q.QAQGSEEEEENRSTRTLEQEIARL.E.GSRQLQ..QRLIQEQIRQDREQRL.GKVENNEGKG
Retrocopy EAR<EQQPQAQGSEEEEENRSTRTLEQEIARL*EDGSRQLQD*QRLIQEQIRQDREQRLTGKVENNEGKG

Parental  TPKLKLKWKCKKEDESQGGYSKDVLLRLLQKYGEVLNLVISSKKAGTAVVEFATVKAAELAFRNEVGLVD
          TPKLKL.WKCKKEDESQGGYSKDVLLRLLQKYGEVLNLVISSKKAGTAVVEFATVKAAELAFRNEVGLVD
Retrocopy TPKLKLNWKCKKEDESQGGYSKDVLLRLLQKYGEVLNLVISSKKAGTAVVEFATVKAAELAFRNEVGLVD

Parental  NPLKISWLEGQPQDTAGPSHPELSKGSVLSERDYESLVMMRMRQAAERQQLIAQMQQEDKGQL
          NPL.ISWLEGQPQ.TAGPSHPELSKGSVLSERDYESLVMMRMRQA.ERQQLIA.MQQEDKGQL
Retrocopy NPL-ISWLEGQPQGTAGPSHPELSKGSVLSERDYESLVMMRMRQAVERQQLIA*MQQEDKGQL

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	6.56 RPM
SRP017611_kidney	0.00 RPM	9.00 RPM
SRP017611_liver	0.00 RPM	5.31 RPM
SRP040447_lung	0.03 RPM	12.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_693 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_693 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693 ,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,