RetrogeneDB ID: retro_cpor_1427

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_80:611902..612607(-)
• Located in intron of: ENSCPOG00000010567

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAM1
• Ensembl ID: ENSCPOG00000027549
• Aliases: None
• Description: None

Sequence

>retro_cpor_1427
TTCCTGCGGGGCATGGCCTTCGTCCCCTTCTTGCTGGTGATCTGGTCGTCGGCCGCAGTCATCATCTCCTACGTGGTGGC
TGTGCTGTCTGGGCACGTGAACCCCTTCCTGCCCTACATCAGCGATACGGGAACAGTCCCACCAGAGAGCGGCATTTTTG
GATTCATGATAAACTTCTCTGCATTTCTTGGCACGGCCACGATATACATGAGATATAAAATCTTGGAGAAGCAGAATGAA
ACCAGCTACTTAAGCACGCCTGTCCTCAACCTGGTGTCGTTAGTTCTTGGCCTGGTGGGCTGCATTGGCATGGGCATCGT
GGCTAACTTCCAGGAGCTGACCATGCCCGTGGTCCATGACGGCGGCGCCCTGCTTGCCTTTGTGTGCGGTGTGATGTACA
TCCTCTTGCAGTCCGTCATCTCCTACAAGTCCTGTCCCCAGTGGAACAGCCTGGCCACATGCCACACCCGGATGGCCATC
TCTGTGGTGTCCTGTGCAGCTGTCCTCCCCATGATCGCCTGTGCCTCCCTGATCTCTATCACCAAGCTGAAGTGGAATCC
GAAAGAAAAGGATTATGTGTATCACCTCGTCAGCGCCATCTGCGAGTGGACCGCGGCCTTTGGTTTCATTTTCTACTTCC
TGACTTTTATCCAAGATTTTCAGAGCGTGACCCTAAGGATATCCATAGAAACCAACGGGGACATC

Alignment

ORF - retro_cpor_1427 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLRKSQKKPLVVTRGSDSLFLLFAVLRIEPGELPTFLLSLSDTGTTPPESGIFGLMINFSAFLGAATMYT
          .LR.....P......S........V.....G....FL...SDTGT.PPESGIFG.MINFSAFLG.AT.Y.
Retrocopy FLRGMAFVPFLLVIWSSAAVIISYVVAVLSGHVNPFLPYISDTGTVPPESGIFGFMINFSAFLGTATIYM

Parental  RYKIVQKQSQLGPRGTQLLNAVSLGLGLAGCVGMGIVANFQELAVPVVHDGGALLAFVCGVVYTLLQSVI
          RYKI..KQ.......T..LN.VSL.LGL.GC.GMGIVANFQEL..PVVHDGGALLAFVCGV.Y.LLQSVI
Retrocopy RYKILEKQNETSYLSTPVLNLVSLVLGLVGCIGMGIVANFQELTMPVVHDGGALLAFVCGVMYILLQSVI

Parental  SYKSHPRWNSLSTCHTRMAISAVSCAAVVPMIACASLISITKLEWNPKEKDYVYHVVSAVCEWTVAFGFI
          SYKS.P.WNSL.TCHTRMAIS.VSCAAV.PMIACASLISITKL.WNPKEKDYVYH.VSA.CEWT.AFGFI
Retrocopy SYKSCPQWNSLATCHTRMAISVVSCAAVLPMIACASLISITKLKWNPKEKDYVYHLVSAICEWTAAFGFI

Parental  FYFLTFIQDFQNVTLRISTEINGDL
          FYFLTFIQDFQ.VTLRIS.E.NGD.
Retrocopy FYFLTFIQDFQSVTLRISIETNGDI

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	0.23 RPM	0.23 RPM
SRP017611_kidney	0.00 RPM	0.84 RPM
SRP017611_liver	0.04 RPM	1.92 RPM
SRP040447_lung	0.08 RPM	63.13 RPM
SRP040447_skeletal_muscle	0.07 RPM	0.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1427 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1427 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027549	1 retrocopy	retro_cpor_1427 ,
Nomascus leucogenys	ENSNLEG00000006362	2 retrocopies	retro_nleu_143, retro_nleu_2841,
Tursiops truncatus	ENSTTRG00000017217	1 retrocopy	retro_ttru_189,