RetrogeneDB ID: retro_xtro_62

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL182080.1:10003..10876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ahcy
• Ensembl ID: ENSXETG00000019486
• Aliases: None
• Description: adenosylhomocysteinase [Source:Jamboree;Acc:XB-GENE-950017]

Sequence

>retro_xtro_62
ACCTGGTACACGCGCATGAGCGCCGAGATCATCGGCGTGACCGAGGAGACCACCACCGGCGTGCACCGCCTGAACGAGAT
GTCTGCCAAGGGCACCTTGCTGTTCCGCGCCATCAACGTGAACGATTCCGTGACCAAGAGCAAGTTCGACAACCTGTACG
GCTGCCGCGAGTCGCTGGTGGACGGCATCAAGCGCGCCACCGACGTGATGATCGCCGGCAAGGTGGCGGTGGTGGCCGGC
TATGGCGACGTGGGCAAAGGCTGCGCCCAGGCCCTGGCCGCGCTGCGCGCCCAGGTGTGGGTCACGGAAATCGACCCCAT
CAACGCGCTGCAGGCCGCCATGGAAGGCTTCAAGGTCGTCACCATGGAATACGCCGCCGACAAGGCCGACATCTTCGTAA
CCACCACCGGCAACAAGGATGTGATCCGCCACGAGCACATGGTGGCGATGAAGAACGAGGCCATCGTCTGCAACATCGGC
CACTTCGACAACGAGATCGACGTGGCGTCGATCGAGAAATACCAGTGGGAGGAAGTCAAGCCCCAGGTGGATCACGTGAT
CTTCCCGGACGGCAAGCGCATCACCCTGCTGGCCAAGGGCCGCCTGGTCAACCTGGGCTGTGCCACGGGCCACCCGAGTT
TCGTCATGTCCAGCTCCTTCGCCAACCAGACCATCGCCCAGATCGAGCTATTCACCAAGCCCGATGCCTACCAGTCCGGC
AAGGTCTACGTGCTGCCCAAAATCCTCGACGAGAAGGTAGCGCGCCTGCACCTGAAGAAAGTCGGCGCCCAACTCACCGT
GCTGAGCGACGCGCAGGCCGCCTACATCGGCGTGAAGAAGGAAGGCCCGTACAAGGCCGATACCTACCGCTAT

Alignment

ORF - retro_xtro_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 67.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKYPQLLKGIKGISEETTTGVHNLYKMKASGTLQVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVM
          T.Y......I.G..EETTTGVH.L..M.A.GTL...AINVNDSVTKSKFDNLYGCRESL.DGIKRATDVM
Retrocopy TWYTRMSAEIIGVTEETTTGVHRLNEMSAKGTLLFRAINVNDSVTKSKFDNLYGCRESLVDGIKRATDVM

Parental  IAGKVAVVAGYGDVGKGCAQALRAFGARVIITEIDPINALQAAMEGYEVTTMEEASKEGNIFVTTTGCTD
          IAGKVAVVAGYGDVGKGCAQAL.A..A.V..TEIDPINALQAAMEG..V.TME.A.....IFVTTTG..D
Retrocopy IAGKVAVVAGYGDVGKGCAQALAALRAQVWVTEIDPINALQAAMEGFKVVTMEYAADKADIFVTTTGNKD

Parental  IVEGSHFENMKDDSIVCNIGHFDCELDVKWLNDNAVKKVNIKPQVDRYLLKNGRHIILLAEGRLVNLGCA
          .....H...MK...IVCNIGHFD.E.DV..........V..KPQVD......G..I.LLA.GRLVNLGCA
Retrocopy VIRHEHMVAMKNEAIVCNIGHFDNEIDVASIEKYQWEEV--KPQVDHVIFPDGKRITLLAKGRLVNLGCA

Parental  MGHPSFVMSNSFTNQVMAQIELWTNNDKYPVG-VYFLPKKLDEAVAAAHLDKLGVKLTKLTDKQAKYLGL
          .GHPSFVMS.SF.NQ..AQIEL.T..D.Y..G.VY.LPK.LDE.VA..HL.K.G..LT.L.D.QA.Y.G.
Retrocopy TGHPSFVMSSSFANQTIAQIELFTKPDAYQSGKVYVLPKILDEKVARLHLKKVGAQLTVLSDAQAAYIGV

Parental  EKEGPFKPDHYRY
          .KEGP.K.D.YRY
Retrocopy KKEGPYKADTYRY

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	65.43 RPM
SRP007412_heart	0.00 RPM	81.15 RPM
SRP007412_kidney	0.00 RPM	81.15 RPM
SRP007412_liver	0.04 RPM	944.38 RPM
SRP007412_skeletal_muscle	0.00 RPM	140.55 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_62 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_62 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 18 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
Callithrix jacchus	ENSCJAG00000018303	7 retrocopies	retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Homo sapiens	ENSG00000101444	6 retrocopies	retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Otolemur garnettii	ENSOGAG00000016787	3 retrocopies	retro_ogar_3223, retro_ogar_3401, retro_ogar_3402,
Pongo abelii	ENSPPYG00000010935	9 retrocopies	retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes	ENSPTRG00000013414	7 retrocopies	retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Tarsius syrichta	ENSTSYG00000007163	3 retrocopies	retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus	ENSTTRG00000003632	1 retrocopy	retro_ttru_1666,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62 ,