RetrogeneDB ID: retro_cpor_1084

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:11753298..11753738(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP11L
• Ensembl ID: ENSCPOG00000001043
• Aliases: None
• Description: None

Sequence

>retro_cpor_1084
GTGGTGGCAGCTTTTCACAAGGCAACTGTGTGCTGGCAGCAAGAACAACAAAAGTGAAGCCAGCCTGGCTTTCAGAAAGC
CCTGGCCTATTGGAAGTAAAGAAAGATTACAAACTTCATGCAGATGACTGTCATGAAAAACAAGAATTCTTCAATGATCT
TTGAAAGAAGCCTCTTGAAAAAAAATCCAAATGAATTCTATTACAAAATGATTTGGCTAAAGATCCAGGTTGGAGTTCAC
ATTACTAAGGAAACTAAAGAAGAATTAACTCTAGGACAGCTAATGAGGACTCAAGATGTCAGATACATAGAAATGAAAAT
GGTTGCAGAAGCTAAGAAAATCTCAGAGCGCCATCTGCTGGATATTCAGGGAAAGCAACAGAATAAGCATGCATTCTGTT
TGACACGCAAAAAGAAATCGAACGGTTTGACGTTGCCACC

Alignment

ORF - retro_cpor_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.18 %
• Parental protein coverage: 60.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAFRKAAKSRQREHRERSQPGFRKHL-GLLEKKKDYKLRADDYHKKQEFLKALRKKALEKN-PDEFYY
          ..AAF.KA....Q.E....SQPGF.K.L.GLLE.KKDYKL.ADD.H.KQEF...L.KK.L....P.EFYY
Retrocopy VVAAFHKATVCWQQEQQK*SQPGFQKAL<GLLEVKKDYKLHADDCHEKQEFFNDL*KKPLXXX>PNEFYY

Parental  KMTRVKLQDGVHVIKDTKEEVTPEQLKLMRTQDVKYIEMKRIAEAKKIERLKSELHLLDFQGKQQGKHVF
          KM...K.Q.GVH..K.TKEE.T..Q..LMRTQDV.YIEMK..AEAKKI....SE.HLLD.QGKQQ.KH.F
Retrocopy KMIWLKIQVGVHITKETKEELTLGQ--LMRTQDVRYIEMKMVAEAKKI----SERHLLDIQGKQQNKHAF

Parental  -FFDTKKEVEQFDIAT
          ..FDT.KE.E.FD.AT
Retrocopy <LFDTQKEIERFDVAT

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	11.33 RPM
SRP017611_kidney	0.00 RPM	24.39 RPM
SRP017611_liver	0.00 RPM	14.45 RPM
SRP040447_lung	0.00 RPM	11.07 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1084 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1084 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	ENSCPOG00000001043	1 retrocopy	retro_cpor_1084 ,
Microcebus murinus	ENSMICG00000001496	1 retrocopy	retro_mmur_894,
Myotis lucifugus	ENSMLUG00000001003	1 retrocopy	retro_mluc_2386,
Mus musculus	ENSMUSG00000028907	1 retrocopy	retro_mmus_1968,
Oryctolagus cuniculus	ENSOCUG00000007154	2 retrocopies	retro_ocun_1285, retro_ocun_669,
Otolemur garnettii	ENSOGAG00000016492	2 retrocopies	retro_ogar_3229, retro_ogar_3324,
Rattus norvegicus	ENSRNOG00000007174	1 retrocopy	retro_rnor_1838,