RetrogeneDB ID: retro_cpor_1341

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_70:2791135..2792035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSF2
• Ensembl ID: ENSCPOG00000007509
• Aliases: None
• Description: None

Sequence

>retro_cpor_1341
AAAATTATAAGTAGTGCTCAGAAGCTTCAGATAAAGCAAGAAACTATTGAGTCCAGGCTTTCAGAACTAAAAAGTGAGAA
CAAGTCCCTCTGGAAGGAGGTGTCAGAACTAAGAGCAAAGCATGCACAACAGCAGCAGGTCATCTGAAAGATTGTCCAGT
TTATTGTTACACTGGTTCAGAAGAACCAGCTTGTGAGCTTAAAACGTAAGAGGCCTCTACTTCTAAATATTAATGGAGTG
CAAAAGAAGAATCTGTTTCAACACATCGTCAAAGAACCAGCTGATAATCACCACCACAAAGTCCCACATAGTAGGACTGA
AGGTTTAAAAGCAAAGGGAGCAGGTTTCAGATGACATCATCATTTATGATGTCAGTGATGGTAATGCAGATGAGGAAAAT
ATCCCAGTTATTCTGGAAACAAATGAGGATGTTATACCTGATCCCTCCAACTGCAGCCAGTACCCTGACATTGTCATTGT
TGAGGACAACAATGAAGATGAATACACACCTGTCATTCAGAGCAGCGAGCTGACAGACTTGACCAGAGAGTCCCCGAGTC
CAGGCAGTGATGGCAGCAGCCCTCTCATGTCCAGTGCTATCCAGCTAAACGGGTCCTCCAGTCTGACAACTGAAGACCCC
GTGACCATGATGGTCTCCATTCTCAATGACAACATTAACCTTCTGGGAAAGGTCGAGCTGCTGGACTACCTTGACAGCAT
CAACTGCAGCCTGGAAGACTTCCAAGCCATGCTGTCGGGCAGACAGTTTAGCATCGACCCGGACCTCCTCGTTGATTCTG
AGAATAAAGTACTGGAAGCTACCAAGAATAATGTTGTTCAGCCAGTTTCTGAAGAAGGAAGAAAATCGAAGTCCAAACCA
GACAAGCAGCTCATCCAGTA

Alignment

ORF - retro_cpor_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.31 %
• Parental protein coverage: 56.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KIISSAQKVQIKQETIESRLSELKRNCSENESLWKEVSELRAKHAQQQQVIRKIVQFIVTLVQNNQLVSL
          KIISSAQK.QIKQETIESRLSELK...SEN.SLWKEVSELRAKHAQQQQVI.KIVQFIVTLVQ.NQLVSL
Retrocopy KIISSAQKLQIKQETIESRLSELK---SENKSLWKEVSELRAKHAQQQQVI*KIVQFIVTLVQKNQLVSL

Parental  KRKRPLLLNTNGAQKKNLFQHIVKEPADNHHHKVPHSRTEGLK-QRERVSDDIIIYDITDDNADEENIPV
          KRKRPLLLN.NG.QKKNLFQHIVKEPADNHHHKVPHSRTEGLK.QRE.VSDDIIIYD..D.NADEENIPV
Retrocopy KRKRPLLLNINGVQKKNLFQHIVKEPADNHHHKVPHSRTEGLK>QREQVSDDIIIYDVSDGNADEENIPV

Parental  IPETNEDVISDPSN--QYPDIVIVEDDNEDEYAPVIQSSEPTDSTRESPSPGGDGSSPLMSSAVQLNGSS
          I.ETNEDVI.DPSN..QYPDIVIVED.NEDEY.PVIQSSE.TD.TRESPSPG.DGSSPLMSSA.QLNGSS
Retrocopy ILETNEDVIPDPSNCSQYPDIVIVEDNNEDEYTPVIQSSELTDLTRESPSPGSDGSSPLMSSAIQLNGSS

Parental  SLTTEDPVTMMDSILNDNINLLGKVELLDYLDSIDCSLEDFQAMLSGRQFSIDPDLLVDLFTSSVQMNPT
          SLTTEDPVTMM.SILNDNINLLGKVELLDYLDSI.CSLEDFQAMLSGRQFSIDPDLLVD...........
Retrocopy SLTTEDPVTMMVSILNDNINLLGKVELLDYLDSINCSLEDFQAMLSGRQFSIDPDLLVDSENKVLEATKN

Parental  DYINNTKSE-NKVLEATKNNVVQPV
          ........E..K..E........PV
Retrocopy NVVQPVSEE<RKKIEVQTRQAAHPV

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	0.52 RPM	19.04 RPM
SRP017611_kidney	0.21 RPM	10.47 RPM
SRP017611_liver	0.17 RPM	5.75 RPM
SRP040447_lung	0.23 RPM	15.79 RPM
SRP040447_skeletal_muscle	0.42 RPM	29.81 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1341 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1341 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010951	1 retrocopy	retro_chof_621,
Cavia porcellus	ENSCPOG00000007509	1 retrocopy	retro_cpor_1341 ,
Macaca mulatta	ENSMMUG00000007910	1 retrocopy	retro_mmul_867,
Tupaia belangeri	ENSTBEG00000013569	3 retrocopies	retro_tbel_1029, retro_tbel_19, retro_tbel_3,