RetrogeneDB ID: retro_tbel_1515

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4948:313045..313713(-)
• Located in intron of: ENSTBEG00000008420

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_1515
ATGGTGCCAGTTAGGCCAGCAGCGAGGCGGTGGACTAGGAGTTTTGGGACAGGCGGTGAAGGGGCTTCTCGGTATGATTC
AGAAATAAGGTGAAACAGAGGCTGTGGTGGCTTAACAGTCTGCAAGCCTGCGTTGGGAGCATTCGCGAGGGACAAGGCTT
TGATTTCGAAGAAAATTTAAGATTCAGCAAAATTACAGGAAATTATTTTGGAAGGAAAAGAAGGCTCAAACATCATAGGA
CTTCCAGTTCACAGATTGATAACCAGATCATCTGAAACATCTCTATTTAGCTGAAGAGGAAAGGCTCAAGAAGCAACTAA
GAAAAGTTGACAAGCCTTTGTCAGAAGTTGATCAGCTTTTGCCTGAAGAACAATGTAGTACTGACCAGGCTTGGTCTAAA
GGTCCGTGTAGTGCTCACCAGTCTCAGCCAGAAGAGCAGTGTAGCCAGCCAGTAAATTCTGTTACAATTCCAAAGAAAAA
GAAAACTTCAAATCAGAAAGCACAAGAAGAGTATGAATAGGTACAAGCTAAGAAATAAGAATTTGAGAGAAGAAAACAAG
AGAGTTCAAAGGCTCTACCAAAAAAAAAAAAAAAAAAAAGGAAGTGTTTAAATATTGAGCTAAAAGACTAAAAAGGGCCA
ACCAAACTTGAATTTACAAATGGAGTAT

Alignment

ORF - retro_tbel_1515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 96.27 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPTRPVARRRTGSLGTGGEGASL-VGFRSKKVKQRTWRPNGLQARVGSIREGQGFAF-RRKLKIQQSYR
          M.P.RP.ARR.T.S.GTGGEGAS..V.FR.K.VKQR.W..N.LQA.VGSIREGQGF.F.RRK.KIQQ.YR
Retrocopy MVPVRPAARRWTRSFGTGGEGASR<V*FRNK-VKQRLWWLNSLQACVGSIREGQGFDF<RRKFKIQQNYR

Parental  KLLRKEKKAQTSQDSQFTDQYPDHLKHLYLAEEERLKKQLRKIDKPLLEEVDRLLPEEQCSTDQAWSKDQ
          KL..KEKKAQTS.D.QFTD..PDHLKHLYLA.EE...K....................QCSTDQAWSK..
Retrocopy KLFWKEKKAQTS*DFQFTD**PDHLKHLYLA-EEERLKKQLRXXXXXXXXXXXXXXXXQCSTDQAWSKGP

Parental  CSTHQPQPEEQCSQPVNSITIPKKNKKKTSNQKAQEEYEQVQAKRAAKKQEFER-RKQEREEAQKLYKKK
          CS.HQ.QPEEQCSQPVNS.TIPKK..KKTSNQKAQEEYE.VQ....AKK.EFER..K.............
Retrocopy CSAHQSQPEEQCSQPVNSVTIPKK--KKTSNQKAQEEYE*VQ----AKK*EFER<KKTREFKGSTXXXXX

Parental  KMEVFK-ILSKKTKKGQPNLNLQMEY
          ..EVFK.ILS.KTKKGQPNLNLQMEY
Retrocopy XXEVFK<ILS*KTKKGQPNLNLQMEY

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_1515 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1515 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,