RetrogeneDB ID: retro_cpor_62

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:24735335..24736289(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000013419
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000026920
• Aliases: None
• Description: None

Sequence

>retro_cpor_62
ATGAATTTGGGGAGTCTAACTACATGGAATCAAACTTCAAGCACTGACTTCATCCTTGTGGGGCTCTTCATGGACACCAA
GCATGCCGCTTTGCTCTACACCATGATCTTCATATTCTTCTTGCTGGCTCTGGCCAGCAGTGCCATTCTCATTGCCCTGA
TCCACTTGGACCTCTGCCTCCACACGCCCATGTACTTCCTCCTCAGCCAGCTGTCACTCATGGACCTCCTAAACATATCC
ATCACGGTGCCCAAGATGCTTGTGGGCCAGGTCACTGGAGATCACACAATTTCCCCCTTGGGCTGTGAGATCCAGATGTC
CTTTTACCTGACCCTGGCTGGGGCTGAGTTCTTCCTCCTAGGAGTGATGGCCTATGACAAATATGCTGCCATTTGCAGGC
CTCTCCACTACCTACTACTGATGAGCCCAAGGGTGTGCCGACTGCTGGCGGACAGTTCCCGGTGTGTGGGGATACTGGAT
GCCCTGCTGATCGCCCTCATCACCCTGAGCTTCCCCTACTGTCAGTCTAGGAGAATCCTGAGCTTCTTCTGTGAAGCCCC
CGCCCTGCTCAAGCTCTCCTGCTCTGACATCTGCCTCTACAGCTTGCTCATGTACTTGTGCTGCGTGCTCATGATCCTGG
TCCCCATCCTGGTCACTTTGGGCTCCTACACCCTGATCCTGTGCCTCATCCAAAGGACGAACTCAGCCAAAGGCCCCAGC
GAGGCCTTTGCCACCTGCTCCTCACACATAATCGTGGTGGTGCTATTCTATGGAGCCACCCTCTATTTCTACATCCTTCC
CAGCCCCTACCACACAGCCCGGCAGGACATGATGGGGTCTGCCTTGTATACAATCATCACGCCAGTGCTGAACCCTCTCA
TCTACAGCCTGCAGAACAAGGATGTCGCAAGGGCCCTGAGCAGCATGGTTCAGCCAAGAGCGAGCTTCAGGAGT

Alignment

ORF - retro_cpor_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSLTPWNQTLSTDFILVGLFMDTKHAALLYTVIFIFFLLALARSALFSVLIHLDLHLHRLMYFLLSQLSL
          GSLT.WNQT.STDFILVGLFMDTKHAALLYT.IFIFFLLALA.SA....LIHLDL.LH..MYFLLSQLSL
Retrocopy GSLTTWNQTSSTDFILVGLFMDTKHAALLYTMIFIFFLLALASSAILIALIHLDLCLHTPMYFLLSQLSL

Parental  MDLLYMPVTVPEILVSQVTGDHTISPSGCGIQIFFYLTQAGAKFFHLGAMAYDQYAAICRPLHYPLLMNH
          MDLL....TVP..LV.QVTGDHTISP.GC.IQ..FYLT.AGA.FF.LG.MAYD.YAAICRPLHY.LLM..
Retrocopy MDLLNISITVPKMLVGQVTGDHTISPLGCEIQMSFYLTLAGAEFFLLGVMAYDKYAAICRPLHYLLLMSP

Parental  RACLLLTTGCWFLGSVDGFMLTSVTMTFPFCGSQEFHHFFCEVPAVTKLSCSDTSLYKTLMYLCCVLMIL
          R.C.LL.......G..D.......T..FP.C.S.....FFCE.PA..KLSCSD..LY..LMYLCCVLMIL
Retrocopy RVCRLLADSSRCVGILDALLIALITLSFPYCQSRRILSFFCEAPALLKLSCSDICLYSLLMYLCCVLMIL

Parental  NPVIVISSSYTSILLTILRMNLEEGWKKALATCSSHMTVVLLFYGVAVYTYMLSSSYHTPQKNMVDSVFY
          .P..V...SYT.IL..I.R.N...G...A.ATCSSH..VV.LFYG...Y.Y.L.S.YHT....M..S..Y
Retrocopy VPILVTLGSYTLILCLIQRTNSAKGPSEAFATCSSHIIVVVLFYGATLYFYILPSPYHTARQDMMGSALY

Parental  TILTPVLNTLIYSFRNKDVTEALNILPQ
          TI.TPVLN.LIYS..NKDV..AL....Q
Retrocopy TIITPVLNPLIYSLQNKDVARALSSMVQ

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_62 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_62 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000026920	1 retrocopy	retro_cpor_62 ,