RetrogeneDB ID: retro_xtro_45

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL177336.1:123..1296(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: acat2
• Ensembl ID: ENSXETG00000021174
• Aliases: None
• Description: acetyl-CoA acetyltransferase 2 [Source:Jamboree;Acc:XB-GENE-5929870]

Sequence

>retro_xtro_45
GAAGATATCGTCATCGTTTCCGCCGTTCGCACGCCTGTGGGCAAGTTTGGTGGCTCCCTCGCCAAGACGCCAGCCTCGGC
GCTCGGCGCCATCGTCATCCAGGAAGCCCTGGCGCGCGCCCAGGTCGGGCTGGATCAGGTTGGCGAGGTCATCCTGGGCC
AGGTACTGGCGGCGGGCTGCGGGCAGAACCCGGCGCGTCAAGCGCTGATAAAGGCTGGCGTGGCCAAGGAAACCCCGGCG
CTGACCATCAACGCCGTATGCGGCTCGGGCCTGAAAGCCGTGATGCTCGCCGCCCAGGCCGTCGCCACTGGCGACAGCGA
GATCGTGGTGGCCGGTGGCCAGGAGAACATGAGCCTGTCGCCGCACATCCTGAATGGCTCGCGCGACGGCCAGCGCATGG
GCGACTGGAAGCTGACCGACACCATGATCGTCGACGGCCTGTGGGACGTGTACAACCAGTACCACATGGGCATCACCGCC
GAGAACGTGGCCAAACAGTACGGCATCACGCGCGACATGCAGGATGCACTGGCCCTGGCCAGCCAGCAGAAGGCCGCCGC
AGCGCAGGACGCTGGCCGCTTTGCCGATGAAATCGTCGGTGTGAGCCTGCCGCAGAAGAAGGGCGATCCGATCCTCTTCA
ACGTGGACGAATACCTCAACCGCAAGACCAGCGCCGAGGCGCTGGCGGGCCTGCGCCCGGCCTTCGACAAGGCGGGCACG
GTGACGGCGGGCAACGCCTCGGGCATCAACGACGGCGCCGCCGCCGTGCTGGTGATGAGCGCCAAAAAGGCCGCCGCGCT
GGGCTTGAAGCCGCTGGCGCGCATCGCCGCCTACGCGACCTCCGGGCTCGATCCGGCCACCATGGGCATGGGGCCGGTAC
CCGCCTCGCGCAAGGCGCTGCAGCGCGCGGGCTGGAATGTGGCGGACGTCGATCTGTTCGAGCTGAACGAAGCCTTCGCA
GCCCAGGCCTGTGCGGTGAACAAGGAACTGGGCATCGACCCGGCCAAAGTCAACGTCAACGGCGGCGCCATCGCCATTGG
CCACCCCATCGGCGCCTCGGGTTGCCGCGTGCTGGTCACGCTGCTGCACGAAATGCAGCGCCGCAACGCCAAGAAGGGTC
TGGCCGCGCTGTGCATCGGCGGCGGCATGGGCGTATCGCTGGCCCTGGAGCGC

Alignment

ORF - retro_xtro_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.96 %
• Parental protein coverage: 98.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERVAIVSAARTPIGSFNGALSTLPAHTLGSTVIKEVLKRAAIQPQEVSEVIFGQVLTAGAGQNPARQASV
          E...IVSA.RTP.G.F.G.L...PA..LG..VI.E.L.RA......V.EVI.GQVL.AG.GQNPARQA..
Retrocopy EDIVIVSAVRTPVGKFGGSLAKTPASALGAIVIQEALARAQVGLDQVGEVILGQVLAAGCGQNPARQALI

Parental  AAGVPYSIPAWSCQMICGSGLKAVSLGAQSIKTGEADIVVAGGMESMSQAPHLVH-MRAGVKAGDVSLQD
          .AGV....PA......CGSGLKAV.L.AQ...TG...IVVAGG.E.MS..PH.....R.G...GD..L.D
Retrocopy KAGVAKETPALTINAVCGSGLKAVMLAAQAVATGDSEIVVAGGQENMSLSPHILNGSRDGQRMGDWKLTD

Parental  SIMCDGLNDAFYKYHMGITAENVAKQWKVTREEQDLLAVQSQNRTEAAQKAGYFDKEIVPVTVPSRKG-P
          ....DGL.D....YHMGITAENVAKQ...TR..QD.LA..SQ....AAQ.AG.F..EIV.V..P..KG.P
Retrocopy TMIVDGLWDVYNQYHMGITAENVAKQYGITRDMQDALALASQQKAAAAQDAGRFADEIVGVSLPQKKGDP

Parental  VEVKVDEFPRHGSNVEAMSKLKPYFLKDGSGTVTPANASGINDGAAAVILIKESEARRRGLVPMAHIVSS
          ....VDE........EA...L.P.F..D..GTVT..NASGINDGAAAV.......A...GL.P.A.I...
Retrocopy ILFNVDEYLNRKTSAEALAGLRPAF--DKAGTVTAGNASGINDGAAAVLVMSAKKAAALGLKPLARIAAY

Parental  AQVGLDPSIMGVGPIAAIRKAVEKAGWSLDEVDLFEINEAFAAQAVAVVKDLGLNPEKVNCQGGAVALGH
          A..GLDP..MG.GP..A.RKA...AGW....VDLFE.NEAFAAQA.AV.K.LG..P.KVN..GGA.A.GH
Retrocopy ATSGLDPATMGMGPVPASRKALQRAGWNVADVDLFELNEAFAAQACAVNKELGIDPAKVNVNGGAIAIGH

Parental  PLGMSGCRILVTLLYALERTGGKKGVAALCIGGGMGIAMCIER
          P.G.SGCR.LVTLL....R...KKG.AALCIGGGMG.....ER
Retrocopy PIGASGCRVLVTLLHEMQRRNAKKGLAALCIGGGMGVSLALER

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	9.35 RPM
SRP007412_heart	0.00 RPM	3.04 RPM
SRP007412_kidney	0.00 RPM	3.04 RPM
SRP007412_liver	0.00 RPM	29.48 RPM
SRP007412_skeletal_muscle	0.00 RPM	1.60 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_45 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_45 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45 ,