RetrogeneDB ID: retro_tbel_129

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1219:210788..211291(+)
• Located in intron of: ENSTBEG00000016153

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSTBEG00000006726
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_tbel_129
GCATGTGCTGCCATTGGGGACTACAATGGCTATGCAGACGTGGCTGTGAAGTACTCAAACAAGGCATCCACTGCCATCTG
AGGGGCCACCATCCTGGTCAAGTTCTTCATCATCCCTGTGCGGAAAGGCTATTGGGGAATAAGATCAGCAAGCCCTACAC
TGTCCCTTGCAAGGTGACTGGTCACTATGGTTCTGTGCTGGTGTGGTTCAACCTGGATCTCAGAGGTACTGGCATTGTCT
TGGTCCCTGTGCCCAAAAAGCTGCTGCTGATGGCTGGTATGGATGACTGCTATACTGTGACCAGGGAGTCTACTGCCACC
CTGGGCAGCTCACCCAAGGCCACCTTTGATGCCATCTCCAAGACCTTCAGTTATCTGAGCCCTAAACTCTGGAAAGAGAC
TGTGTTCACCAAGTCTCCCTATCAGGAATTCACTCAGCATCTTGTCAAGACCTGTACCAGAGTTTCCATGCAGGAGACCT
GGGCTCCAGCTGTGGCCACAACA

Alignment

ORF - retro_tbel_129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWG-NKIGKPHTVPCKVTGRCGSVLVR
          A..AIGDYNG.....VK.S....TAI.GA.IL.K..I.PVR.GYWG.NKI.KP.TVPCKVTG..GSVLV.
Retrocopy ACAAIGDYNGYADVAVKYSNKASTAI*GATILVKFFIIPVRKGYWG<NKISKPYTVPCKVTGHYGSVLVW

Parental  LIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKS
          .....RGTGIV..PVPKKLL.MAG.DDCYT..R..TATLG...KATFDAISKT.SYL.P.LWKETVFTKS
Retrocopy FNLDLRGTGIVLVPVPKKLLLMAGMDDCYTVTRESTATLGSSPKATFDAISKTFSYLSPKLWKETVFTKS

Parental  PYQEFTDHLVKTHTRVSVQRTQAPAVATT
          PYQEFT.HLVKT.TRVS.Q.T.APAVATT
Retrocopy PYQEFTQHLVKTCTRVSMQETWAPAVATT

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_129 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_129 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 10 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Callithrix jacchus	ENSCJAG00000015267	15 retrocopies	retro_cjac_1482, retro_cjac_1585, retro_cjac_1609, retro_cjac_1712, retro_cjac_1964, retro_cjac_2201, retro_cjac_2255, retro_cjac_2284, retro_cjac_2361, retro_cjac_2493, retro_cjac_2620, retro_cjac_274, retro_cjac_317, retro_cjac_3741, retro_cjac_4194,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Gorilla gorilla	ENSGGOG00000009371	5 retrocopies	retro_ggor_129, retro_ggor_1391, retro_ggor_1428, retro_ggor_168, retro_ggor_390,
Microcebus murinus	ENSMICG00000012765	28 retrocopies	retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Nomascus leucogenys	ENSNLEG00000008877	1 retrocopy	retro_nleu_2895,
Otolemur garnettii	ENSOGAG00000010098	19 retrocopies	retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri	ENSTBEG00000006726	30 retrocopies	retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129 , retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,