RetrogeneDB ID: retro_cpor_1328

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:3551560..3552101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEBL1
• Ensembl ID: ENSCPOG00000002998
• Aliases: None
• Description: None

Sequence

>retro_cpor_1328
CTGGTCTGCTGCGGAAAGGTGGTCATCCTCGAATACCACACTTCAGGGAAGGTATCTTGGGCACATCAGTTTGTGGAAGG
TGAGTTCTTTGGAGGCTGCATTCCTACAGTAGAGAATACTCACAGCAATAGTCTGTCCTGGCAAAGATGAGTTCGCCTCC
ACCTGGTGGACAGAGCAGTACAGGATGAGTATAGCATTCTGCCTTATTCATTCATCACTGGGATCCTTGGTAATGTGTTT
GTATATTCTGTTACCTCTCTGCATAGCTTTCCAAGTCACTAAGAGTCTCTACCAAATACTACACAAAGATCATAGAAAGT
CCCTGTTGCTGGTGGTGCTAGTATGAAACAAAGCAGAGCTTTCTCCAGATAGACAGGTGCAGGCCACCAAAGGGAAGAAA
CTAGCAGAGTCCTGGAGTATAATATTTATGGGATCATCAGCTTAAGAGAGTCAGATGATTCAAAGCATCTTCACTAGAGT
TATCCAGGAGATTGTCCATGTGGACAATTCCTGTGGGCAAGAGCATCGGTGCTATGTCCTG

Alignment

ORF - retro_cpor_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.99 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVRYRKVVILGHRSVGKTSLAHQFVKGEFLECYDPTVENAYSKIVTLGKDEFHLHLVDTAGQDEYSILPY
          LV...KVVIL.....GK.S.AHQFV.GEF.....PTVEN..S...........LHLVD.A.QDEYSILPY
Retrocopy LVCCGKVVILEYHTSGKVSWAHQFVEGEFFGGCIPTVENTHSNSLSWQR-*VRLHLVDRAVQDEYSILPY

Parental  SFIVGIHGYVLVYSVTSLHS-FHIIENLYQKLHQGHGKTQLPVVLVGNKADLSSDREVQAVQGKKLAESW
          SFI.GI.G.V.VYSVTSLHS.F.....LYQ.LH..H.K..L.VVLV.NKA.LS.DR.VQA..GKKLAESW
Retrocopy SFITGILGNVFVYSVTSLHS>FQVTKSLYQILHKDHRKSLLLVVLV*NKAELSPDRQVQATKGKKLAESW

Parental  GATFMESSAREHQLTQSIFTRVIQEIARVENSYEQDHRCCLM
          ...FM.SSA.E.Q..QSIFTRVIQEI..V.NS..Q.HRC...
Retrocopy SIIFMGSSA*ESQMIQSIFTRVIQEIVHVDNSCGQEHRCYVL

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	0.92 RPM
SRP017611_kidney	0.00 RPM	0.52 RPM
SRP017611_liver	0.00 RPM	0.91 RPM
SRP040447_lung	0.05 RPM	1.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1328 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1328 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328 ,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Erinaceus europaeus	ENSEEUG00000008514	2 retrocopies	retro_eeur_338, retro_eeur_528,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802,
Otolemur garnettii	ENSOGAG00000013477	1 retrocopy	retro_ogar_2338,
Pan troglodytes	ENSPTRG00000004897	1 retrocopy	retro_ptro_115,
Rattus norvegicus	ENSRNOG00000021571	1 retrocopy	retro_rnor_2059,