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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggagagatagtataattttttgttagaaaagtgattgtcttatctaactcttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT

Basic information

species Glycine max
transcript GLYMA08G09170.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 15
lower sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggagagatagtataattttttgttagaaaagtgattgtcttatctaactcttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT
                                                                                                                       ||| |        |          | | |  | |  |  |  | |||||  ||   |  ||    |    || |   |||||| |||||||||||| | || ||||| ||||| ||||| || ||| | || ||||| |||||||| ||||| ||||| ||||| |||||  |||| | 
-----------------------------------------------------------------------------------------------------------------------gtaaagagccccatc-------caactcttcttttcagttgattcttttacttcact--aacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 15
lower sequence: AT1G31070.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggagagatagtataattttttgttagaaaagtgattgtcttatctaactc-ttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT
                                                                                         |  | | | | |  ||    |      |  || |  || ||| ||       | | | |  | || |||   ||  ||||  || |||| ||  ||         || |||||| || || |||||  | || || || || || ||||| || ||| | || |||||||||||||| ||||||||||||||||| || ||  |||| | 
-----------------------------------------------------------------------------------------gtaactctcaaaacaaatcttctcattactgtgtttttatttatt-------ttacttttctgtccaacgaatttatttttcttatatgcaaaatcgaataaat-tttagGTGTAGAGGTTTCACCTTTGTGCTCATACGCCGGAGAAAATCTTGAAGCTATTTGTCGAGGAAGAACGTTTCATGCACCTTGTGAAATTTCCCTCTAATG

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 14
gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggag-agatagtataattttttgttagaaaagtgattgtcttatctaactcttccttttctttttatggaatgtcccgccctc---------attcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT
                                                                                                            ||  |  | | |  ||  || |   ||  ||  ||  | |   || |  |||| |  | |  ||  ||||   |||  ||   |             ||||||| ||  | ||||||||||| || ||| |||| |||||||| ||| | || || || |||||||||||||| || |||||||| ||||| ||||||  
------------------------------------------------------------------------------------------------------------ataaatcatacataattcttctcattttcaatggtagtggcactaacagactcatattctatttgatatgtggtgtggcggtgtttgatgtggaggccagGTGTGGAGATATCACCACTCTGCTCCTATTCTGGGGAAAACCTAGAAGCCATCTGCCGTGGAAGAACATTTCACGCTCCTTGTGAAATCTCATTCTAGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|254342038|gb|GR853175.1|GR853175
EST:     AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAG                         GTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
genomic: AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAGgtaagttatt ... cctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
EST: gi|8282791|gb|BE020352.1|BE020352
EST:     AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAG                         GTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
genomic: AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAGgtaagttatt ... cctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
EST: gi|193334482|gb|FK301730.1|FK301730
EST:     GTTGTCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAG                         GTGTTGAAGTGTCACCAC
genomic: GTTG-CTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAGgtaagttatt ... cctcattcagGTGTTGAAGTGTCACCAC
EST: gi|298176684|gb|HO026805.1|HO026805
EST:     AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAG                         GTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
genomic: AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAGgtaagttatt ... cctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA
EST: gi|151397105|gb|EV266978.1|EV266978
EST:     AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAC                         GTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTA
genomic: AGTTGCTGCAGGTGGCTTCTTAACACATTCAGTGCCCTTATATGCAACAGgtaagttatt ... cctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtcttatctaactcttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT
        atctaac  putative branch site (score: 2)
                                       tcccgccctcattc  putative PPT
                     ttttctttttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggagagatagtataattttttgttagaaaagtgattgtcttatctaactcttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC