RetrogeneDB ID: retro_cpor_195

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:72362827..72363549(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNFT1
• Ensembl ID: ENSCPOG00000014736
• Aliases: None
• Description: None

Sequence

>retro_cpor_195
ACAGACTTCTCAGAATTACGCTGTCTTCTCAAGTGCTTGCAAAAATGCCTTCCATAGATTTTTGATACTGTCAAACTTTA
AATGCAGCATATAAAAGAAATGTCTCTTGGAATTGGTCTGCCAACAACTTTTATATAAGCAAATGAAAGCATTGTAAATC
AGATTTTTCCAAGAGAATGATCCTCAAAGATTCAGTGTGCTTAGTTGTTGGTATTCTTAGCAGAATCTTCTGTTCTTTTG
TACTGTACCTTTCATTCTGAGTCACTTTATTTACAGCTTAGTTTTCTTGAATCCTACACTGGATCCTTTGAGCTTCTGGG
AAGTACTTTGAATTGTTGGAATTATAGACTTCAATCTGCAATTCCTCTTCATGGGCTTAAAATGCCTTATTTTATTGATG
CCTTCTTTCATCGTGCCTTTTAAATCAAAGAGTTACTGGTGTATGCTTTTAGAAGAATTATGTCAGTGTTGCCAAACTTT
TGTTCCCCTGCCGGTTTGGTTCTCTTACCATATAAACTACAGGGAGTTGGATAATGGAACTAGGTAGAGTCTTGGGATAT
TGATGGCATTTCTCTACCTCATCCTTAAACTTTTGGATATTTTTGGACATTTGGGAACTTTTAGACAGGTTTTATGTTTA
TTTTTTACAAGACCAAGTTATGGAGTAGTTGCCAGCATGAGACAGTTTTCGGGTGTGGATGATAATTTGTTCAACATGTC
AG

Alignment

ORF - retro_cpor_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.49 %
• Parental protein coverage: 57.66 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSFSEFRYLLKWLQKCLPYILILSVKLFMQHLTGISLGIGLLTTFMYANKSIVNQVFLRERSSKIHCAWL
          ..FSE.R.LLK.LQKCLP.I....VKL.MQH....SLGIGL.TTF..AN.SIVNQ.F.RE.SSKI.CA.L
Retrocopy TDFSELRCLLKCLQKCLP*IFD-TVKL*MQHIKEMSLGIGLPTTFI*ANESIVNQIFPRE*SSKIQCA*L

Parental  LVFLAGSSILLYYTFHSQSLY-YSLIFLNPTLDHLSFWEVLWIVGITDFILKFLFMGLKCLILLVPSFIM
          LVFLA.SS.LLY.TFHS.SLY.YSL.FLNPTLD.LSFWEVL.IVGI.DF.L.FLFMGLKCLILL.PSFI.
Retrocopy LVFLAESSVLLYCTFHSESLY>YSLVFLNPTLDPLSFWEVL*IVGIIDFNLQFLFMGLKCLILLMPSFIV

Parental  PFKSKGYWYMLLEELCQYYRTFVPTPVWFRYLISYGELGNVTRWSLGILLALLYLILKLLDFFGHLRTFR
          PFKSK.YW.MLLEELCQ...TFVP.PVWF.Y.I.Y.EL.N.TR.SLGIL.A.LYLILKLLD.FGHL.TFR
Retrocopy PFKSKSYWCMLLEELCQCCQTFVPLPVWFSYHINYRELDNGTR*SLGILMAFLYLILKLLDIFGHLGTFR

Parental  QVLRIFFTRPSYGVAASKRQCSDVDD-ICSICQ
          QVL..FFTRPSYGV.AS.RQ.S.VDD.ICS.CQ
Retrocopy QVLCLFFTRPSYGVVASMRQFSGVDD>ICSTCQ

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	0.06 RPM	7.36 RPM
SRP017611_kidney	0.00 RPM	12.56 RPM
SRP017611_liver	0.00 RPM	12.36 RPM
SRP040447_lung	0.05 RPM	15.06 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_195 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_195 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009747	2 retrocopies	retro_btau_1229, retro_btau_413,
Cavia porcellus	ENSCPOG00000014736	1 retrocopy	retro_cpor_195 ,
Sus scrofa	ENSSSCG00000017671	2 retrocopies	retro_sscr_1201, retro_sscr_523,