RetrogeneDB ID: retro_xtro_11

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172701.1:305048..305987(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000003833
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: hnrnpa3
• Ensembl ID: ENSXETG00000001806
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:Jamboree;Acc:XB-GENE-5878765]

Sequence

>retro_xtro_11
GTTTCAATGAGTACCGGCGATATGGATACGACGCAACTCTGCAAACTGTTTATCGGGGGGCTTAACGTGCAGACCACCGA
AGAGGGCCTACGCCAGCATTTTGAGACCTACGGTCAACTGACGGACTGCGTGGTGGTTATCAACCCACAGACCAAGCGGT
CTCGATGTTTCGGTTTCGTAACCTACTCGAGTGCCGCGGAGGCCGACGCGGCGGTGGAGGCCTCGCCCCACGTGGTTGAC
GGTAACAACGTTGAGCTGAAGCGGGCCGTCTCCAGGGAAGATTCCGCCAAGCCGGGGGCACACGCTAAAGTGAAGAAGCT
CTTTGTTGGCGGCCTGAAAGAGGACGTCGGCGAGAGTGACTTGCTCGAACACTTCGCCCAGTTTGGCGCCGTGGAAAAAG
TGGAGATCATTGCCGATAAAGTGTCCGGCAAGAAACGCGGCTTCGGCTTTGTGTACTTTACCAACCACGATTCCGCCGAC
AAGGCCGCGGTGGTCAAGTTCCACTCCATCAACGGGCACCGCGTCGAGGTAAAGAAGGCCGTGCCCAAGGAGGAACTTTC
CCAGGGTTCCAATAGATCCTTCCGCGGCGGCAGGGGCGGGAGAGGCCGAGGTGGCGGCGGAGCGCCCCGGGACTACAATG
GCATCCCTGGAAGTGGCGGCAAAGCTGCTTTCGGTGGGGGCTACGGCGGCTATGGGGGCGGCAACCAGGGCTACGGCTCG
TACGGAGGCGGCTATGGCGAGCAGAGCGACTACGGCAATGGCTACAACAGTTTCGGGAGCTACAGCCAGCACCAGTCCTC
GTACGGGCCCATGAAGGGAGCGGGAAGCGGCAGCTGGAACCGGCCCAACACGTCAGGCCCCTACCGCGGAGGTTATAGCG
GCGGCGGCGGAGGAGGAGGTTATGGCGTCGGCAGCTCCTATGGCGGCGGCTCCTTCTGA

Alignment

ORF - retro_xtro_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.44 %
• Parental protein coverage: 79.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLRKLFIGGLSFETTDDSLREHFEQWGKLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDG
          QL.KLFIGGL...TT...LR.HFE..G.LTDCVV...PQTKRSR.FGFVTYS...E.DAA..A.PH.VDG
Retrocopy QLCKLFIGGLNVQTTEEGLRQHFETYGQLTDCVVVINPQTKRSRCFGFVTYSSAAEADAAVEASPHVVDG

Parental  RVVEPKRAVSREDSARPGAHLTVKKIFVGGIKEDTEEYHLRDYFQSYGKIETIEVMEDRQSGKKRGFAFV
          ..VE.KRAVSREDSA.PGAH..VKK.FVGG.KED..E..L...F...G..E..E...D..SGKKRGF.FV
Retrocopy NNVELKRAVSREDSAKPGAHAKVKKLFVGGLKEDVGESDLLEHFAQFGAVEKVEIIADKVSGKKRGFGFV

Parental  TFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQTASAQRGRGGGGSNFMGRGG---NYGGGGGGGGN
          .F..HD..DK..V.K.H.INGH..EVKKA..K.E....S....RGG.G....G.GG....Y.G..G.GG.
Retrocopy YFTNHDSADKAAVVKFHSINGHRVEVKKAVPKEELSQGSNRSFRGGRGGRGRGGGGAPRDYNGIPGSGGK

Parental  FGRGGGFGNRGGYGGGGGGGRGGGYGSGGD--GGYNGFGGEGGNYGGGPGYGGRGYGGSPGYGNQGGGYG
          ...GGG.G..GG.G..G.G..GGGYG...D...GYN.FG.............G.G..GS....N..G.Y.
Retrocopy AAFGGGYGGYGG-GNQGYGSYGGGYGEQSDYGNGYNSFGSYSQHQSSYGPMKGAG-SGSWNRPNTSGPYR

Parental  GGGSGGGGGGYDGYNEGGNFGGGNY
          GG.SGGGGGG..GY..G...GGG..
Retrocopy GGYSGGGGGG--GYGVGSSYGGGSF

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	38.63 RPM	277.77 RPM
SRP007412_heart	23.80 RPM	183.56 RPM
SRP007412_kidney	23.80 RPM	183.56 RPM
SRP007412_liver	49.18 RPM	243.45 RPM
SRP007412_skeletal_muscle	7.03 RPM	115.15 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_11 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_11 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 30 parental genes, and 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11 ,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,