RetrogeneDB ID: retro_xtro_18

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172711.1:405918..406164(+)
• Located in intron of: ENSXETG00000027230

Retrocopy information

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

Parental gene information

• Parental gene symbol: gtf2a2
• Ensembl ID: ENSXETG00000022002
• Aliases: None
• Description: general transcription factor IIA, 2, 12kDa [Source:RefSeq peptide;Acc:NP_001005107]

Sequence

>retro_xtro_18
ATGGCTTATCAACCGTACAGGATTACAACACTAGGTAACAGTCTCCAGGAGAGCCTGGATGAGTTAATACAGTTTCAGCA
GATCAACTCTCAATTTGCACTTAAGTTTCTGTTAAAGTTTAACAAGGCTATTAATTCTGCATTGCCATAGTGGGTTAGAA
GGAGGGTCAACTTCAGGGGATTCTTGAAAAACTATAGGTTTTGTGATAATATATGGACCTTTGTGTTTAAAAAAGTTGAG
TTGAGA

Alignment

ORF - retro_xtro_18 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.39 %
• Parental protein coverage: 75.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYQLYRNTTLGNSLQESLDELIQSQQINPQLALQVLLQFDKAINSALAQRVRNRVNFRGSLNTYRFCDN
          MAYQ.YR.TTLGNSLQESLDELIQ.QQIN.Q.AL..LL.F.KAINSAL...VR.RVNFRG.L..YRFCDN
Retrocopy MAYQPYRITTLGNSLQESLDELIQFQQINSQFALKFLLKFNKAINSALP*WVRRRVNFRGFLKNYRFCDN

Parental  VWTFVLNDVEFR
          .WTFV...VE.R
Retrocopy IWTFVFKKVELR

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	0.13 RPM
SRP007412_kidney	0.00 RPM	0.13 RPM
SRP007412_liver	0.09 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_18 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_18 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 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010298	1 retrocopy	retro_btau_1649,
Canis familiaris	ENSCAFG00000016665	2 retrocopies	retro_cfam_786, retro_cfam_912,
Cavia porcellus	ENSCPOG00000000816	1 retrocopy	retro_cpor_525,
Dipodomys ordii	ENSDORG00000007867	3 retrocopies	retro_dord_377, retro_dord_385, retro_dord_695,
Homo sapiens	ENSG00000140307	1 retrocopy	retro_hsap_4034,
Macaca mulatta	ENSMMUG00000018428	1 retrocopy	retro_mmul_2303,
Monodelphis domestica	ENSMODG00000011636	1 retrocopy	retro_mdom_1563,
Otolemur garnettii	ENSOGAG00000007061	1 retrocopy	retro_ogar_1752,
Ochotona princeps	ENSOPRG00000012841	1 retrocopy	retro_opri_908,
Pan troglodytes	ENSPTRG00000007129	1 retrocopy	retro_ptro_2734,
Rattus norvegicus	ENSRNOG00000011062	2 retrocopies	retro_rnor_1021, retro_rnor_1141,
Sorex araneus	ENSSARG00000012228	2 retrocopies	retro_sara_607, retro_sara_734,
Sus scrofa	ENSSSCG00000004583	3 retrocopies	retro_sscr_545, retro_sscr_934, retro_sscr_935,
Ictidomys tridecemlineatus	ENSSTOG00000004010	3 retrocopies	retro_itri_1631, retro_itri_440, retro_itri_925,
Tupaia belangeri	ENSTBEG00000001053	9 retrocopies	retro_tbel_1162, retro_tbel_1207, retro_tbel_123, retro_tbel_1394, retro_tbel_1439, retro_tbel_257, retro_tbel_2655, retro_tbel_2737, retro_tbel_513,
Xenopus tropicalis	ENSXETG00000022002	1 retrocopy	retro_xtro_18 ,