RetrogeneDB ID: retro_tbel_2975

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_12567:60921..61508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSTBEG00000001316
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_tbel_2975
CTGTCGTGGTTTGACAGCTCTGAATTAGGGTTCTCACTGGAATACCCCATTATTAGTTTACATGCTGTGTCCAGGTCCAG
GGATCTGAAATACCTATCTGTGAGAACATTTGTATGTTATGGTGAATGCCAGATTTGGAGAAGAATCAAAAGAATCTGTT
GATGAAGAAGAGGAGGAAGACAGTGATGATGACGTTGAACCTATTACTTAATTTGGATTTGTGCCTATTGATAAATCAGC
ATTGGAGGCCCTGTTCACTGCCATGTGTGAATGCCAGGCCTTGCACCGGATCCTGAGGCTAAAGATTCAGATGATTACGA
TGGAGACAAGTATGATGTGGAGGCACACGGACAAGGATAGGGGAACACCCCTACATTTTACACCTATGGAGAAGGGTTAT
CTCACTTCACAGCAGAAGGAAGGCCATACTGGAGAGATTAGAAGGAATGCTTTCTCAGTCTGTGAGCAGCCAGTATAATA
TGGCAGGGTTCAGGACAAAAGTTTCAATAAGAGATTATGAAAATGGGATGGAGATAGACACCACACCAATGCTTGCTGGA
CAGTTTGAGGACGTAGATGTTGACCAC

Alignment

ORF - retro_tbel_2975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSWLDGSGLGFSLEYPTISLHAVSR--DL-NAYPREHLYVMVNARFGEESKESVDEEEEEDSDDDVEPIT
          LSW.D.S.LGFSLEYP.ISLHAVSR..DL.N.Y..EHLYVMVNARFGEESKESVDEEEEEDSDDDVEPIT
Retrocopy LSWFDSSELGFSLEYPIISLHAVSRSRDL>NTYL*EHLYVMVNARFGEESKESVDEEEEEDSDDDVEPIT

Parental  EFRFVPSDKSALEALFTAMCECQALH-PDPEDEDSDDYDGEEYDVEAHEQDRGDIPTFY-YEEGLSHLTA
          .F.FVP.DKSALEALFTAMCECQALH.PDPE..DSDDYDG..YDVEAH.Q..G..PTFY.Y.EGLSH.TA
Retrocopy *FGFVPIDKSALEALFTAMCECQALH<PDPEAKDSDDYDGDKYDVEAHGQG*GNTPTFYTYGEGLSHFTA

Parental  EG-QGTLERLKRMLSQSVKRQNIMDGVRTE-DIK-YEDGMEIDTTPTVAGQFEDADVDH
          EG....LERL..MLSQSV..Q..M.G.RT...I..YE.GMEIDTTP..AGQFED.DVDH
Retrocopy EG<KAILERLEGMLSQSVSSQYNMAGFRTKVSIRDYENGMEIDTTPMLAGQFEDVDVDH

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_2975 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2975 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Choloepus hoffmanni	ENSCHOG00000007254	1 retrocopy	retro_chof_1685,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Dasypus novemcinctus	ENSDNOG00000008188	1 retrocopy	retro_dnov_477,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Myotis lucifugus	ENSMLUG00000024623	2 retrocopies	retro_mluc_1501, retro_mluc_1507,
Mustela putorius furo	ENSMPUG00000015944	1 retrocopy	retro_mputfur_435,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Tupaia belangeri	ENSTBEG00000001316	1 retrocopy	retro_tbel_2975 ,