RetrogeneDB ID: retro_tbel_972

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3458:588633..589225(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSTBEG00000008887
• Aliases: None
• Description: coiled-coil domain containing 59 [Source:HGNC Symbol;Acc:25005]

Sequence

>retro_tbel_972
ATGGAACTGGTCAGGCCATCAGTGAGGTGGCAGACTGAGAGTTTTGGGACGGGCGGCCCCGAAAGGGTTTCTCAGGTAGG
GTTCAGGAATAAGGTGAAACAGAGGACGTGGTGGCCTAGCAGCCAGCAAGCCTGCATGGAGAGCATTCACAAGGGACAAG
ACCTTGCATTTTGAAGAAAATTTAAGATTCAGCAAAATGATAGGAAATTATTATGGAAGGAAAAGAAGGCTCAAACATCA
CAGGACTCCCAATTCACAGATCGATACCCAGATCACCTGAAACATCTCTATTTAGCTGAGGAGAAAAGACTCAAGAAGCA
ACTAAGGAAAGTTGACAAGCCTTTGTTAGAAGAAGTCGATCAGCTTTTGCCTGAAGAACAATGTAGGACTGACCAGGCTT
GGTCTAAATGTCAGTGCTCGCCAGCCTCAGCCAGAAGAATAGTGTAGACAACCAGTAAAGTCCATTACAATTCTAAAGAA
AACATCAAATCAGAAAGCACAAGAATATGAACAGGTACAAGCTAAGCATGCTGCTAAGAAATAAGAATTTGAGAGAAGAA
AACAAGAGACAGAAGAGGCTCAAAGGCTCTAC

Alignment

ORF - retro_tbel_972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 84.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPTRPVARRRTGSLGTGG-EGASLVGFRSKKVKQRTWRPNGLQARVGSIREGQGFAFRRKLKIQQSYRK
          M...RP..R..T.S.GTGG.E..S.VGFR.K.VKQRTW.P...QA...SI..GQ..AF.RK.KIQQ..RK
Retrocopy MELVRPSVRWQTESFGTGGPERVSQVGFRNK-VKQRTWWPSSQQACMESIHKGQDLAF*RKFKIQQNDRK

Parental  LLRKEKKAQTSQDSQFTDQYPDHLKHLYLAEEERLKKQLRKIDKPLLEEVDRLLPEEQCSTDQAWSKDQC
          LL.KEKKAQTSQDSQFTD.YPDHLKHLYLAEE.RLKKQLRK.DKPLLEEVD.LLPEEQC.TDQAWSK.QC
Retrocopy LLWKEKKAQTSQDSQFTDRYPDHLKHLYLAEEKRLKKQLRKVDKPLLEEVDQLLPEEQCRTDQAWSKCQC

Parental  S-THQPQPEEQCSQPVNSITIPKKNKKKTSNQKAQEEYEQVQAKRAAKKQEFERRKQEREEAQKLY
          S...QP...E.C.QPV.SITI.KK....TSNQKAQ.EYEQVQAK.AAKK.EFERRKQE.EEAQ.LY
Retrocopy S>QPQPE--E*CRQPVKSITILKK----TSNQKAQ-EYEQVQAKHAAKK*EFERRKQETEEAQRLY

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_972 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_972 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 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972 ,