RetrogeneDB ID: retro_tbel_2715

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_117363:107475..108261(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSTBEG00000002918
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_tbel_2715
ATGGCTCGGGGCCCTAAGAAGCATCTGAAGCGGGTTGCAGCTCCAAAACATTGGATGCTAGATAAATTGACTGGTGTGTT
TGCCCCTCGTCCATCCACTGGTCCCCACAAGCTGAGGGAATGTCTTCCTCTCATCATTTTCCTAAGGAACAGACTTAAGT
ATACTTTAACAGGAGACGAAGTAAAGATCTGCATGTAGCGGTTCATTAAGATTGATGGCAAAGTCCATACTGACATAACC
TACCCTGCTGGTTTCATGGATGTCATCAGCATTGACAAGACCGGAGAGAATTTCCGACTGATCTATGACACCACGGGTCG
CTTTGCTGCCCATGGTATTACACCTGAGGAGGTCAAGTACAAGTTGTGCAAAGTGAGGAAAATCTTTGTGGGCACAAAAA
GAACCCCTCATTTGGTGACCCATGATGCTTGTACCATCCGCTACCCGGATCCTCTCATCAAGGTGAATGACACCATTCAG
ATTGACTTGGAGATGGGCAAGATTACTGATTTTATCAAGTTTGATACCAGTAACCTGTGTATGGTGACTGGAGGTGCTGA
CTTGGGAAGAATTGGTGTGATCACCAACAGAGAGAGGCATCCTGGCTCTTTTGATGTGGTTCATGTGAAAGATGCCAATG
GCAACAGCTTTGCCACTCGGCTCTCCAACATTTTTGTTATTGGCAAAGGCAACAAGCAATGGATTTCTCTTCCCCGGGGA
AAAGGTATCCACCTCACCATTGCCGAAGAGAGAGACAAGAGACTGGCAGCCAAACAGAGCAGTGGG

Alignment

ORF - retro_tbel_2715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFI
          MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKY.LTGDEVK.ICM.RFI
Retrocopy MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYTLTGDEVK-ICM*RFI

Parental  KIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLV
          KIDGKV.TDITYPAGFMDVISIDKTGENFRLIYDT.GRFA.H.ITPEE.KYKLCKVRKIFVGTK..PHLV
Retrocopy KIDGKVHTDITYPAGFMDVISIDKTGENFRLIYDTTGRFAAHGITPEEVKYKLCKVRKIFVGTKRTPHLV

Parental  THDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHV
          THDA.TIRYPDPLIKVNDTIQIDLE.GKITDFIKFDT.NLCMVTGGA.LGRIGVITNRERHPGSFDVVHV
Retrocopy THDACTIRYPDPLIKVNDTIQIDLEMGKITDFIKFDTSNLCMVTGGADLGRIGVITNRERHPGSFDVVHV

Parental  KDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG
          KDANGNSFATRLSNIFVIGKGNK.WISLPRGKGI.LTIAEERDKRLAAKQSSG
Retrocopy KDANGNSFATRLSNIFVIGKGNKQWISLPRGKGIHLTIAEERDKRLAAKQSSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2715 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2715 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 16 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus	ENSFCAG00000012041	11 retrocopies	retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Macaca mulatta	ENSMMUG00000003295	7 retrocopies	retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Tupaia belangeri	ENSTBEG00000002918	20 retrocopies	retro_tbel_1108, retro_tbel_1367, retro_tbel_1465, retro_tbel_1798, retro_tbel_2241, retro_tbel_2659, retro_tbel_2711, retro_tbel_2715 , retro_tbel_2722, retro_tbel_2743, retro_tbel_2944, retro_tbel_310, retro_tbel_3172, retro_tbel_3232, retro_tbel_4263, retro_tbel_4569, retro_tbel_4572, retro_tbel_4648, retro_tbel_511, retro_tbel_877,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,