RetrogeneDB ID: retro_cpor_108

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:5101649..5102588(-)
• Located in intron of: ENSCPOG00000025321

Retrocopy information

• Ensembl ID: ENSCPOG00000021330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000025321
• Aliases: None
• Description: Taste receptor type 2 [Source:UniProtKB/TrEMBL;Acc:H0W6H8]

Sequence

>retro_cpor_108
AGTCTCTTATCAATAATGGGTAGTGTCACACTGAGCATATTTACTATAATTTTTAGTGTGAAGTTCATATTTGGAAACTT
AGGAAATATATTTATAATCCTGGTGAACTGCATGGACCTGATCAACACAAGAAAGATCTCTTTAGCTGATCACCTGCTCA
CTGCTTTGGCAATCTCCAGGGTTGGTCTGATCTGGGTGTTATTCTCAAGTTGGTGGAGGGACATGTTTTTTCCCAATTTC
TGGATGAATTTAATAATGGTAAGAACAATGTATATTATTTGGATTGTGACTTGTCATTTTAACATATGGCTTGCCACATG
CCTCAGCATCTTTTATTGCCTCAAGGTAGCCAATTTTTCCAACTCTATTTTTCTTTATTTTAAGTGGAGAGTCAAAAAGG
TGATTTCAGTGACATTGCTGGTGTCTCTTGTTGTCTTGCTTTTATACCTTTTGCAGTCAAATACACATATGAATGTCTTG
ATTGATGAGCATAAAAGAAACATATCTTACAACTCCAGCTTACAGAACTTTCCTGAGTTTTCAAAACTTGTCTTACTCAG
CAACACTATGTTCACATTCATAGCCTTTGCTCTGTCCTTGACGACTTTTCTCCTGCTCATCTTCTCCCTGTGGAAACATC
TGAAGAGGATGCAGCACAGTGTCAGAGGGTCCAGAGATGCAAGCACCACAGCCCACATAAACGCCTTGCAAGCTGTGGTT
GCCTTTCTCCTCCTGTACACAACTTTCTTTCTGTCTATTTTAACAGAACTTTGGATAACTAAGTTTCCAAACATTCTCTA
TTTTTACTTTTGTCTGGCTGGTGAAATTGCTTTTCCTTCAGTTCACTCATTTGTCCTAATCTTGGTGAACAGTAAGTTAA
AACAGGCCTGTCTTCCAGTGTTGAGCTGGCTAAGGTGTGGTTCCAAAGATGAATCCCCA

Alignment

ORF - retro_cpor_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.28 %
• Parental protein coverage: 97.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGVMPSIFRLVFSVEFTIGNLGNVFIILVNCMDLINRRKISLADQLLTALAISRIVLLWILFTSWWLHL
          M..V..SIF...FSV.F..GNLGN.FIILVNCMDLIN.RKISLAD.LLTALAISR..L.W.LF.SWW...
Retrocopy MGSVTLSIFTIIFSVKFIFGNLGNIFIILVNCMDLINTRKISLADHLLTALAISRVGLIWVLFSSWWRDM

Parental  FSPGFYMNFVRLRLSYAIWSMTFHFNAWLATCLSIFYCLKIANFSNSMFLYFKWRVKKVVLVTLLASTFL
          F.P.F.MN....R..Y.IW..T.HFN.WLATCLSIFYCLK.ANFSNS.FLYFKWRVKKV..VTLL.S..L
Retrocopy FFPNFWMNLIMVRTMYIIWIVTCHFNIWLATCLSIFYCLKVANFSNSIFLYFKWRVKKVISVTLLVS--L

Parental  VIFDKYIIAIHIEMNVWHDESKRNVSYSFNLKNFKQFPGALLSISSMFMLIPFTMSLIACLLLIFSLWKH
          V....Y.......MNV..DE.KRN.SY...L.NF..F....L....MF..I.F..SL...LLLIFSLWKH
Retrocopy VVLLLYLLQSNTHMNVLIDEHKRNISYNSSLQNFPEFSKLVLLSNTMFTFIAFALSLTTFLLLIFSLWKH

Parental  LKKMQHNAKGSRNASTTAHRKAMQTVISFLLLYAIYLFCLIMQITSFKFLEKDHIIFFEHAVG--IAVPS
          LK.MQH...GSR.ASTTAH..A.Q.V..FLLLY..............KF.....I..F.......IA.PS
Retrocopy LKRMQHSVRGSRDASTTAHINALQAVVAFLLLYTTFFLSILTELWITKF---PNILYFYFCLAGEIAFPS

Parental  GHSLVLILGNRKLRQAFFSVVWWLRSRPK
          .HS.VLIL.N.KL.QA...V..WLR...K
Retrocopy VHSFVLILVNSKLKQACLPVLSWLRCGSK

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_108 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_108 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000025321	2 retrocopies	retro_cpor_108 , retro_cpor_791,