RetrogeneDB ID: retro_cpor_656

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_21:16888236..16889348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKCI
• Ensembl ID: ENSCPOG00000015212
• Aliases: None
• Description: None

Sequence

>retro_cpor_656
CCAAGAAAAGATAAACCCATCTACTGCAGAGCTGCATGCCTCTAGAGAAAGCTTTATTATGCAAATGGGCACACTTTTCA
AGCCAAAGGTTTCATTCAGCAGTCGTGCTGATTGTACCATCTTCTCAGTCCATACAGGGTGGCTTGGATGCTAGATATAC
AAGTGTATCAACTGTAAACTTTTGGTTCATATGAAGTGCCACACACTTGTCACAATTGAATGCAAGCAGCATTTTTTGCC
ACCAGAACCCATGATGACAATGGATCGATCACCCATGTCTTTAGACCCTGCACAGATAGTAATTCTATATAATCCCAAAA
GTCATAAAGGTTTGGAAGAATTAGATGAAGGGAATGAGGCAGGGAACAACTGGGAAAAGTGTATGAAAGCTTTGTCCAGT
TTTGATCTTCATCTTTAGGACCTTTGATTTGCTTTGAGTAATAGGGAGAGGAAGTTATGCAAAAGTACTATTAACTGAAT
TTTTAAAAAGACATTGCATCTATGCAATGAAAGTTCTGAAAAAAAACCAGCCTGCTGACATTGACCAGATGTAGACAAAG
AAGCATGTTTTGGAGCAAGTATCAATTACTCTTTTCTTGTTGGATTGCAATCTTGCTCTTAGACAGAAAGCAATCTATTC
CCTGTTCTAGCCCATGTAAGTGGAGGAGATCTAATGTGTTATATGCAGCAACAAGGAATACTTCCTGAAGACCATGCCAG
GTTTTACTCTGTAAAAACCAGGTTAGCATTTGGTTTTCTTCATGTGCAAGGGATAATATACAGAAATTTTAAATTGGACA
ATTTATTTCTGGACTCAAAAATTAAACTCACTGACTATTGGTTGTGTTAGGAAGGACTACAGCCAGGAGACAAGACCAGC
ACTTTCTGTGGCACTCCTAACTACCTTGCTCTAGAAATTCTAAGAGGAGAAGATTATTGTTCCAGTGTGGACAGGTGGAC
CCTTGGAGTACTGTTTGAGATGATGGTTGGCAAGTCTCCATTTCATCTTGTTGGGAGCCCTGATAACCCTGATTACAACA
CAAAAAACAATCTCTTGCAAGTCATTTTGGAAAGAAAAAATTCACATCCCATGTTGTCTGTCTGTATATGCA

Alignment

ORF - retro_cpor_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.67 %
• Parental protein coverage: 65.54 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGEDKSIYRRGARRWRKLYCANGHT-FQAK-RFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKL
          P..DK.IY.R.A...RKLY.ANGHT.F..K..F..RA.C.I.......LG...YKCINCKLLVH.KCH.L
Retrocopy PRKDKPIYCRAACL*RKLYYANGHT>FKPKVSFSSRADCTIFSVHTGWLGC*IYKCINCKLLVHMKCHTL

Parental  VTIECGRHSLPPEPMMQMDQSSMHSDHAQTVIPYNPSSH---ESLDQVGEEKEAMNTRESGKASSSLGLQ
          VTIEC..H.LPPEPMM.MD.S.M..D.AQ.VI.YNP.SH...E.LD...E.............S..L.L.
Retrocopy VTIECKQHFLPPEPMMTMDRSPMSLDPAQIVILYNPKSHKGLEELDEGNEAGNNWEKCMKALSSFDLHL*

Parental  D-FDLLRVIGRGSYAKVLLVRD-RIYAMKVVKKELVNDDEDIDWVQTEKHVFEQAS-NHPFLVGLHSCFQ
          D.FDLL.VIGRGSYAKVLL............K........DID...T.KHV.EQ.S.N..FLVGL.SC..
Retrocopy D>FDLL*VIGRGSYAKVLLTEFLKRHCIYAMKVLXXXQPADIDQM*TKKHVLEQVS<NYSFLVGLQSCS*

Parental  TESRLFFVIEYVNGGDLMFHMQRQRKLPEEHASFNSAEISLALNYLHERGIIYRDLKLDNVLLDSEGHIK
          TES.LF.V...V.GGDLM..MQ.Q..LPE.HA.F.S....LA...LH..GIIYR..KLDN..LDS...IK
Retrocopy TESNLFPVLAHVSGGDLMCYMQQQGILPEDHARFYSVKTRLAFGFLHVQGIIYRNFKLDNLFLDSK--IK

Parental  LTDYGMCKKEGLRPGDTTSTFCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNP
          LTDY..C..EGL.PGD.TSTFCGTPNY.A.EILRGEDY..SVD.W.LGVL.FEMM.G.SPF..VGS.DNP
Retrocopy LTDYWLC*-EGLQPGDKTSTFCGTPNYLALEILRGEDYCSSVDRWTLGVL-FEMMVGKSPFHLVGSPDNP

Parental  DQNTEDYLFQVILEK-QIRIPRSLSVKA
          D.NT...L.QVILE...I.IP..LSV.A
Retrocopy DYNTKNNLLQVILER>KIHIPCCLSVYA

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	43.42 RPM
SRP017611_kidney	0.00 RPM	17.27 RPM
SRP017611_liver	0.00 RPM	7.66 RPM
SRP040447_lung	0.00 RPM	25.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_656 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_656 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015212	1 retrocopy	retro_cpor_656 ,
Homo sapiens	ENSG00000163558	1 retrocopy	retro_hsap_4884,
Pongo abelii	ENSPPYG00000014289	1 retrocopy	retro_pabe_3798,
Pan troglodytes	ENSPTRG00000015615	1 retrocopy	retro_ptro_3254,