RetrogeneDB ID: retro_tbel_4373

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_79229:1227..1725(-)
• Located in intron of: None

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_4373
GTCGCCATCGGGGACTACAATGGCCATGTTGGTTTGGACATGAAGTGCTCCAAGGAGGTGGCCACTGCCATCTAAGGGAC
CATCATCTAGGCCAAACTCTCCATTGTCCCAGTGCGGAGAGGCTACTGGGGGGAACAACATCGGCAAGCCCCACACTGTC
CCTTGCAAGGTGACCAGCCACTGTGGCTCTGTGCTGGTGCACCTCATTCCTGCCCTTAGAGGCACTGGCATCGTCTCTGT
CCCTGTGCCCAAGAAGCTGCTGCTGATGGCTGGCATCGATGACTGCTACACCTCAGCCCGGGGCTGCACTGCCACCCTGG
GCAACTTCACCAAGGCCACCTTTGATGCCATCTCCAAGACCTACAGCTATCTGACCCCTGACCTCTGGAAAGAGACTGTG
TTCAACAAGTCTCCCTATCAGGAATTCACTGACCATCTTGTCAAGACCCACACCAGAGTCTCCGTGCAGAGACCCAGCCT
CCAGCTGTGGCCACAACA

Alignment

ORF - retro_tbel_4373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWG-NKIGKPHTVPCKVTGRCGSVLVRLI
          VAIGDYNGHVGL..KCSKEVATAI.G.II.AKLSIVPVRRGYWG.N.IGKPHTVPCKVT..CGSVLV.LI
Retrocopy VAIGDYNGHVGLDMKCSKEVATAI*GTII*AKLSIVPVRRGYWG>NNIGKPHTVPCKVTSHCGSVLVHLI

Parental  PAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPY
          PA.RGTGIVS.PVPKKLL.MAGIDDCYTSARGCTATLGNF.KATFDAISKTYSYLTPDLWKETVF.KSPY
Retrocopy PALRGTGIVSVPVPKKLLLMAGIDDCYTSARGCTATLGNFTKATFDAISKTYSYLTPDLWKETVFNKSPY

Parental  QEFTDHLVKTHTRVSVQR-TQAPAVATT
          QEFTDHLVKTHTRVSVQR.TQ.PAVATT
Retrocopy QEFTDHLVKTHTRVSVQR<TQPPAVATT

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_4373 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4373 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,