RetrogeneDB ID: retro_cpor_1321

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:40779703..40780223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST3GAL6
• Ensembl ID: ENSCPOG00000013240
• Aliases: None
• Description: None

Sequence

>retro_cpor_1321
GGTAGAGAGAGATGTGACCTACCCTGGGGGCGCGCGTCCCGGGTGTGCATCCGGGGTGCGCTTTCCTGGTATTGCGCAGC
TGCGACGGCTCTGAGTATTATGCCAGTGAACCACGCACCTAAGAACGTGGTGCTTGGCAATGGAGGAGTTTCGAGGCATA
AGACATTGTGAGCAAAAATGAACTCCTAAGATGTAATAAAAAGAAGCAATGATGGTCCGGTGTTAGGTCATGAAGAGGAA
GCTGGGAGGAGGACAGCTTTCTGACTTTTTTGTCCAGAAGCTGTTTTTTCCTATCCAGGCACGAGGCTCCTAAGCCACAG
CCATGCTCACTGTTCTTAAGCCACTTGATTTAAAGTGGCTGGGGGAATTGTTAACTGGTGGCAAAATAGACGCTAATGCT
AAAGAAACCAGCCTTAAACTTGATCTATAAACCTTATCAAATAAGAATATTAGATGTTTCCATATCAGGACAGCAGCTTA
GCATCCGCTTCATTTTCCAGGTGTTTCCTAAAAATCAGAA

Alignment

ORF - retro_cpor_1321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.49 %
• Parental protein coverage: 53.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GSNKLYLPY-GIRASEEYFQLALSKLQSCDLFDEFDNEP-CKRCVVVGNGGILKNKTLGEKIDSYDVIIR
          G.....LP..G.R........A...L.SCD.......EP.....VV.GNGG....KTL..K..S.DVI.R
Retrocopy GRERCDLPW<GARVPGVHPGCAFLVLRSCDGSEYYASEP>APKNVVLGNGGVSRHKTL*AKMNS*DVIKR

Parental  MNNGPVLGHEEEVGRRTTFRLFYPESVFSDPS-HSDPN-ATAILTVFKPLDLKWLEELLTGGKINTNGFW
          .N.GPVLGHEEE.GRRT.F.LF.PE.VFS.P..H..P..ATA.LTV.KPLDLKWL.ELLTGGKI..N...
Retrocopy SNDGPVLGHEEEAGRRTAF*LFCPEAVFSYPG<HEAPK<ATAMLTVLKPLDLKWLGELLTGGKIDANA--

Parental  KKPAL-NLIYKPHQIRILDP-FIIRTAAYDLLHFPKVFPKNQ
          K...L.NLIYKP.QIRILD..F.IRTAA...LHFP.V..K..
Retrocopy KETSL>NLIYKPYQIRILDV<FHIRTAA*HPLHFPGVS*KSE

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	9.72 RPM
SRP017611_kidney	0.00 RPM	18.42 RPM
SRP017611_liver	0.00 RPM	12.19 RPM
SRP040447_lung	0.00 RPM	16.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.28 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1321 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1321 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013240	2 retrocopies	retro_cpor_1321 , retro_cpor_1338,
Dipodomys ordii	ENSDORG00000016606	1 retrocopy	retro_dord_15,