RetrogeneDB ID: retro_xtro_65

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL185543.1:385..1303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: etfa
• Ensembl ID: ENSXETG00000015322
• Aliases: None
• Description: electron-transfer-flavoprotein, alpha polypeptide [Source:Jamboree;Acc:XB-GENE-943222]

Sequence

>retro_xtro_65
ATGACTGCACTCGTCATCGCCGAACACGACAATGCTTCGATCAGGCGTGCCACCCTCAACACTGTCACCGCCGCAGCCGC
CTGCAGTGCCGACGTACATATGCTGGTCGCCGGAGAGAACGCCGCTGCCGTTGCCCAGGCAGCCTCCAAAATAGCCAGCG
TCACCAAGGTTCTCCACGCCGACTGTGCCGCCCTGAAGGACGGTCTGGCGGAAAACCTCGCCGCGCAAGTGCTGGCCATT
GCGTCGAACTACAGCCACATCCTGTTTCCGGCCACAACTGGCGGCAAGAACGTGGCCCCACGCGTCGCCGCCAAGCTCGA
TGTGGCGCAGATCAGCGACATCACCAAAGTGGTGAGCCCCGACAGCTTCGAGCGCCCCATCTACGCTGGCAACGCCATTG
CCACCGTGCAATCGGGCGACGCCGTCAAGATCATCACCGTGCGCGGCACCAGCTTTGATGCCGCAGCTGCCACAGGTGGC
AACGCCATGATCGAAACCGTGATCGCCGTCGCCGATAGTGGCAAGAGCAGCTTCGTGGATCGCGAGGTCACCAAGAGTGA
CCGGCCCGAGCTCACGGCCGCCAAGATCATCGTCAGTGGTGGCCGGGCACTGGGCAGCGCCGAGAAATTCAACGAGGTCA
TGATCCCGCTGGCCGACAAGCTTGGCGCTGCCATTGGCGCAAGCCGCGCGGCAGTGGATGCGGGCTACGCCCCGAACGAC
CTGCAGGTAGGGCAGACGGGCAAGATCGTGGCGCCGCAGCTGTACATCGCCTGCGGCATTTCCGGGGCCATCCAGCACCT
GGCGGGTATGAAGGACAGCAAAGTCATCGTGGCCATCAACAAGGATCCCGAGGCGCCGATTTTCGGTGTGGCTGACTATG
GACTGGAGACGGATCTATTCACGGCTGTGCCGGAGATA

Alignment

ORF - retro_xtro_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.31 %
• Parental protein coverage: 92.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSALVIAEHDTQQVTPVTLSAITAAKRLGADVSCLVAGTNCSKVAEELAKVQGVSKLFVAQHESYKGFLP
          ..ALVIAEHD.......TL...TAA....ADV..LVAG.N...VA....K...V.K...A.....K..L.
Retrocopy MTALVIAEHDNASIRRATLNTVTAAAACSADVHMLVAGENAAAVAQAASKIASVTKVLHADCAALKDGLA

Parental  EEELTPLVLEAQKKFNFTHICAGASAFGKSLLPRIAAKLDVAPVSDVIEIKSPDTFVRTIYAGNALCTVK
          E.........A....N..HI...A...GK...PR.AAKLDVA..SD.....SPD.F.R.IYAGNA..TV.
Retrocopy ENLAAQVLAIAS---NYSHILFPATTGGKNVAPRVAAKLDVAQISDITKVVSPDSFERPIYAGNAIATVQ

Parental  CEESVKVFSIRGTSFEAAETSGGSASSDTVAPSAPAGLSEWLHQSLTKSDRPELTSAKVVVSGGRGLKSG
          ....VK....RGTSF.AA...GG.A...TV...A..G.S.......TKSDRPELT.AK..VSGGR.L.S.
Retrocopy SGDAVKIITVRGTSFDAAAATGGNAMIETVIAVADSGKSSFVDREVTKSDRPELTAAKIIVSGGRALGSA

Parental  ENF-KLLYDLADQLNAAVGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKTIV
          E.F......LAD.L.AA.GASRAAVDAG..PND.QVGQTGKIVAP.LYIA.GISGAIQHLAGMKDSK.IV
Retrocopy EKFNEVMIPLADKLGAAIGASRAAVDAGYAPNDLQVGQTGKIVAPQLYIACGISGAIQHLAGMKDSKVIV

Parental  AINKDPEAPIFQVADYGLVADLFKAVPEM
          AINKDPEAPIF.VADYGL..DLF.AVPE.
Retrocopy AINKDPEAPIFGVADYGLETDLFTAVPEI

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	31.92 RPM
SRP007412_heart	0.00 RPM	212.30 RPM
SRP007412_kidney	0.00 RPM	212.30 RPM
SRP007412_liver	0.00 RPM	64.16 RPM
SRP007412_skeletal_muscle	0.00 RPM	159.91 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_65 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_65 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011967	1 retrocopy	retro_mdom_4,
Ochotona princeps	ENSOPRG00000000755	1 retrocopy	retro_opri_1148,
Xenopus tropicalis	ENSXETG00000015322	1 retrocopy	retro_xtro_65 ,