RetrogeneDB ID: retro_cpor_196

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:72802468..72802872(-)
• Located in intron of: ENSCPOG00000021559

Retrocopy information

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

Parental gene information

• Parental gene symbol: MITD1
• Ensembl ID: ENSCPOG00000010970
• Aliases: None
• Description: None

Sequence

>retro_cpor_196
CTGGGGCAGGATGTGGAGGGCACAGCTGCAGTCACTGTGCCAAAGAGGGCAGGAAACTCCACTCCAAGTCCTGGTACCAG
CAGTTCTGGTGTGTCACCAGAAGGGGACTGATCTGCTCCTGTAGGTTCTGAGAGGCAGCAAGGACTATGAAGAAATGCAT
CTCAGAGAAGGGTTTCTGGCTTCAAGGATAGAGCAGGAAACAAAAAATATCAGGACCAAGAAAAAGAAGTTGAAAAACAT
CACAAGCAAATTAAAAGAGAAGACAGTGCAAAAGGTCTGAGTTATGAGTCACTTTGGAAAGAATACCTTAATGAGACACT
ACAGAAGTCTGGATAGTGAGTGCTTATATTGGACATATTCACCAGCTGTATAATTTCCTTCAATTTTGTGAGATGCTTAT
TAAA

Alignment

ORF - retro_cpor_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.34 %
• Parental protein coverage: 55.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IGQDPDSRAAITVLSRAV-ELDSESRYQQ-ALVCYQEGIDLLLQVRKGTQDHSKRCYLRE-KITCYMDRA
          .GQD....AA.TV..RA...L.S.S.YQQ..LVC.Q.G.DLLL.V..G..D......LRE.......DRA
Retrocopy LGQDVEGTAAVTVPKRAG<KLHSKSWYQQ<VLVCHQKGTDLLL*VLRGSKDYEEM-HLRE<RVSGFKDRA

Parental  EDIKKYLDQVKEDGKYHKQIKIEENATGFSYESLFKEYLSGTV-TEVWIEDPYIRQTHQLYNFLRFCEML
          ...KKY.DQ.KE..K.HKQIK.E..A.G.SYESL.KEYL..T..TEVWI...YI...HQLYNFL.FCEML
Retrocopy GN-KKYQDQEKEVEKHHKQIKREDSAKGLSYESLWKEYLNETL<TEVWIVSAYIGHIHQLYNFLQFCEML

Parental  IK
          IK
Retrocopy IK

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	11.79 RPM
SRP017611_kidney	0.00 RPM	14.24 RPM
SRP017611_liver	0.00 RPM	10.23 RPM
SRP040447_lung	0.00 RPM	20.81 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_196 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_196 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010970	1 retrocopy	retro_cpor_196 ,
Otolemur garnettii	ENSOGAG00000002240	1 retrocopy	retro_ogar_883,
Sorex araneus	ENSSARG00000000765	1 retrocopy	retro_sara_766,