RetrogeneDB ID: retro_xtro_25

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173107.1:599031..599379(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: sri
• Ensembl ID: ENSXETG00000008793
• Aliases: None
• Description: sorcin [Source:Jamboree;Acc:XB-GENE-952117]

Sequence

>retro_xtro_25
CTCAAGCAAGCAGGGCTTTCTGGGGATTCAAACCATTTAACCTAGAAGTTGGCCTCCTTATGATCTCTACACTGGATAGG
GATATGTCTGGCAAAATGGGTTTAATCAAAAGAACTGGAGATGATAATAAATAGTTGGAGACAGCACTTCATTATGGATG
ATACTGATGGGAGTGGCACAGTTCAGGGGCATGGACTTCATGTTGTCTCTAGGAATATTGGGATATTGGTTGAGCCCTCC
GGCGCTGAATTTTACAGCAAAAGATCCAGCAGAAATGGAAGATCCACTTTTGATTATCACATTGACTGCTGTGTGAAACT
GTCAGCTCTGAGAGACACATCCAGAAGG

Alignment

ORF - retro_xtro_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.3 %
• Parental protein coverage: 60.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LTQAGLSG-GYKPFSLETCRLMIAMLDRDMSGKMGFNEFKELG-MVINGWRQHFMTYDGDRSGTVEGHEL
          L.QAGLSG.G.KPF.LE...LMI..LDRDMSGKMG....K..G.M.IN.WRQHF...D.D.SGTV.GH.L
Retrocopy LKQAGLSG<GFKPFNLEVGLLMISTLDRDMSGKMGL--IKRTG>MIINSWRQHFIMDDTDGSGTVQGHGL

Parental  HA-ALGAMGYRLSPQALNNIA-KRYSTNGRISFDDYITCCVKLRALTDMFRR
          H...LG..GY.LSP.ALN..A.KR.S.NGR..FD..I.CCVKL.AL.D..RR
Retrocopy HV>SLGILGYWLSPPALNFTA<KRSSRNGRSTFDYHIDCCVKLSALRDTSRR

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	29.36 RPM
SRP007412_heart	0.00 RPM	32.91 RPM
SRP007412_kidney	0.00 RPM	32.91 RPM
SRP007412_liver	0.00 RPM	48.66 RPM
SRP007412_skeletal_muscle	0.00 RPM	9.68 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_25 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_25 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25 ,