RetrogeneDB ID: retro_xtro_60

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181797.1:9243..9789(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: sdhb
• Ensembl ID: ENSXETG00000013435
• Aliases: None
• Description: succinate dehydrogenase complex, subunit B, iron sulfur (Ip) [Source:Jamboree;Acc:XB-GENE-970193]

Sequence

>retro_xtro_60
ATCTCCTTCCGCCGCTCGTGCCGCGAAGGCGTGTGCGGCTCCGACGCCATGAACATCAACGGCAAGAACGGTCTGGCCTG
CCTGACGAACATGAACACCCTGCCGGGCACTATCACTCTCAAGCCCCTGCCCGGCCTGCCGGTGATCCGCGACCTGATCG
TGGACATGACGCAGTTCTTCAAGCAGTACCACTCGATCAAGCCCTACCTGCAGAACGAAACCCCGGTATCGCCATTCAAG
GAGCGCCTGCAATCGCCCGAAGAGCGCGAGGAGCTCAACGGCCTGTACGAATGCATCCTGTGCGCCAGCTGCTCGACGAG
CTGCCCCAGCTTCTGGTGGAACCCCGACAAGTTCGTCGGCCCGGCCGGACTGCTGCAAGCCTACCGCTTCATCGCCGACA
GCCGCGACGAAGCCACGGGCGACCGCCTGGACAACCTGCAGGATCCGTACCGCCTGTTCCGCTGCCACAGCATCATGAAC
TGCGTCGATGTATGCCCGAAGGGCCTGAACCCCACCCGCGCGATTGGCAAGATCAAGGAATTGATG

Alignment

ORF - retro_xtro_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.61 %
• Parental protein coverage: 64.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTFRRSCREGICGSCAMNINGGNTLACTVRIDTNLSKVSKIYPLPHMYVVKDLVPDLSNFYAQYKSIEPY
          ..FRRSCREG.CGS.AMNING.N.LAC.....T.L.......PLP...V..DL..D...F..QY.SI.PY
Retrocopy ISFRRSCREGVCGSDAMNINGKNGLACLTNMNT-LPGTITLKPLPGLPVIRDLIVDMTQFFKQYHSIKPY

Parental  LKKKDESQEGKEQYLQSIEDRDKLDGLYECILCACCSTSCPSYWWNADKYLGPAVLMQAYRWMIDSRDDY
          L.........KE..LQS.E.R..L.GLYECILCA.CSTSCPS.WWN.DK..GPA.L.QAYR...DSRD..
Retrocopy LQNETPVSPFKER-LQSPEEREELNGLYECILCASCSTSCPSFWWNPDKFVGPAGLLQAYRFIADSRDEA

Parental  TEERLAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMM
          T..RL..LQDP..L.RCH.IMNC...CPKGLNP..AI..IK..M
Retrocopy TGDRLDNLQDPYRLFRCHSIMNCVDVCPKGLNPTRAIGKIKELM

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	100.18 RPM
SRP007412_heart	0.00 RPM	151.15 RPM
SRP007412_kidney	0.00 RPM	151.15 RPM
SRP007412_liver	0.00 RPM	74.54 RPM
SRP007412_skeletal_muscle	0.00 RPM	149.43 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_60 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_60 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60 ,