RetrogeneDB ID: retro_xtro_19

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172727.1:2133001..2133386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000032448
• Aliases: None
• Description: None

Sequence

>retro_xtro_19
AGAGCTGATAAAGGAGGCCTCATAGTCATCCTTAATAAAGATGATTATTGAAGCCTATAGACAACTTTCTGATAAGGATT
CCTATAGCACTTTAGAAAAAAATCCTTTAAATGATTATGAAATTGAACTAGATGTCCTCCTTTCAGAAGCTCTCCACTAT
AAAATCATAGATGAAAAGTTATTCTCCTTCTTGAAACCAGACAGACCTCAAGTGGCAATCTTTCACTACTTACCAAAAAC
ACATAAAAAGGAGAGACCGCCACCGGGTAGGCCTATCATAGCAGGTATAGGCTCCCTGGGTGAAAATCTATGTGAATATA
TTGTCTCATATTTACAACCTTTAGTCTTAAGACTACCAAGCTATCTAAAAGATAGTAGTCATCTA

Alignment

ORF - retro_xtro_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 77.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RADKGGLIVILNKND-CEAQRQLSDRLTYKILDKNPLPLFETELDAVLSEEALDFKIIDEKLFSFLKPDK
          RADKGGLIVILNK.D..EA.RQLSD...Y..L.KNPL...E.ELD..LSE.AL..KIIDEKLFSFLKPD.
Retrocopy RADKGGLIVILNKDD>IEAYRQLSDKDSYSTLEKNPLNDYEIELDVLLSE-ALHYKIIDEKLFSFLKPDR

Parental  PQIAIFHYLPKTHKSKRPPPGRPIIAGIGSLGENLCEYIDFYLQPLVLRLPSYLKDSSHL
          PQ.AIFHYLPKTHK..RPPPGRPIIAGIGSLGENLCEYI..YLQPLVLRLPSYLKDSSHL
Retrocopy PQVAIFHYLPKTHKKERPPPGRPIIAGIGSLGENLCEYIVSYLQPLVLRLPSYLKDSSHL

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_19 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_19 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000031345	1 retrocopy	retro_xtro_29,
Xenopus tropicalis	ENSXETG00000032448	1 retrocopy	retro_xtro_19 ,