RetrogeneDB ID: retro_cpor_455

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:31248640..31249103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF1
• Ensembl ID: ENSCPOG00000021163
• Aliases: None
• Description: None

Sequence

>retro_cpor_455
TTTGTCCAGAAACAGAACATTGTCCATTTCCTCACAAATCCACATTATGAACGTCTTATTAATGCAGAGGGCCATGGCAA
AGTGTGGACAGGTTGGAGTGATGATATGCCCAAGTTTTTCCAGTGTGGACAGAGATGTACTACTAATGAGAATTCCTGTT
CTAACCGAACTGTGATGGATAATTGGAACCAGAAAAGATATGATCTAAGGAATATAGTGCAACCCAAACTCTTGCCTTCC
CAGTCTTGACACTACTTTGAAACAATACATGATAAAAGCTACAACAGCAAAATGCCACTTTCAACCCACAGACATAAGCA
AGAGCTGCTTTAGTTCCCAGGATACCAACCTGAACTGAATCCTCCTTGATACAAATGCACAGAAAGTCAACTTACACAAC
TGGCTATTCAAAGCCTCAAATTAGGCATCACTTGGCTGTGCATGGGTTGATAATACTGATAAA

Alignment

ORF - retro_cpor_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.15 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFQKQSLVRFLTNPHYGSLINADGHGEVWIDWNDTS-KFFQYGWRCTTSENSYSNRTLVGNWNQERYDLR
          F.QKQ..V.FLTNPHY..LINA.GHG.VW..W.D...KFFQ.G.RCTT.ENS.SNRT...NWNQ.RYDLR
Retrocopy FVQKQNIVHFLTNPHYERLINAEGHGKVWTGWSDDMPKFFQCGQRCTTNENSCSNRTVMDNWNQKRYDLR

Parental  NIVQPKPLPSQFQHYFETTYDTSYNTKLLLSTHRFKREPHWFPGHQPELDSPPNKCTE-KSVYMSNYSKP
          NIVQPK.LPSQ..HYFET..D.SYN.K..LSTHR.K.E...FPG.QPEL..P..KCTE.KS.Y...YSKP
Retrocopy NIVQPKLLPSQS*HYFETIHDKSYNSKMPLSTHRHKQELL*FPGYQPELNPP*YKCTE<KSTYTTGYSKP

Parental  QIRHHLS-CAWVANTDQ
          QIRHHL..CAWV.NTD.
Retrocopy QIRHHLA<CAWVDNTDK

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	2.53 RPM
SRP017611_kidney	0.00 RPM	4.40 RPM
SRP017611_liver	0.00 RPM	1.39 RPM
SRP040447_lung	0.00 RPM	1.79 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.43 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_455 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_455 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003039	3 retrocopies	retro_chof_1409, retro_chof_1629, retro_chof_888,
Cavia porcellus	ENSCPOG00000021163	1 retrocopy	retro_cpor_455 ,
Erinaceus europaeus	ENSEEUG00000009977	1 retrocopy	retro_eeur_658,
Mus musculus	ENSMUSG00000037971	1 retrocopy	retro_mmus_3061,