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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcaccattaccatattgatcgtaccctcttcctttagattattattactatttttttaatgtttccttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG

Basic information

species Glycine max
transcript GLYMA14G40430.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 4
lower sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
gatcaccattaccatattgatcgtaccctcttcctttagattattattactatttttttaatgtttcc----ttactcata-tagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG
       |  |||| |    | ||  |  |||   | |   | |   ||  ||  | | |||  ||      ||| | ||  |  |||  |  | |  ||||||||| || || ||||| |||||||| ||||| || || || ||||||||||||||||| |||
-----taaaaaccaaacacgtagttacgccttttatgaacctctgtctatgatgctatcaatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG

upper sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
--gatcaccattaccatattgatcgtaccctcttcctttagattattatt-actatttttttaatgtttccttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG
   ||     |   | |  ||| |||    | ||  | || ||||||  | |  ||| | ||  |   |  || |||||  |  |      | | |  | ||||| |||||||||||||| ||||||||||| || || || || |||||||||||||| |||
tgtatgtgtttgggcttgctga-cgtgtagt-ttggtgtatattattgctcatcattatattctttcctttttgctcatggaact-gtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG

upper sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 4
gatcaccattaccatattgatcgtaccctcttcctttagatta--ttattactatttttttaatgtttc-cttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG
 |  |  |   |||| |  ||  |  |     | | ||||||   ||  | | |  | ||||      |  || ||||  |  ||| |     |  | |  |||| ||||| ||||||||||| |||||||| || || || || || |||||||||||||||
taaaaatagagccatgt--ataatgtctataacgtgtagattggtttgcttccaggtgtttagaccaccatttgctcac-tgcttttctttcgttgcatatagGTATATCTAATACTTGATGAGTTCATTCTTGCTGGAGAGCTCCAGGAAACAAGCAAGAAG

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|6846408|gb|AW348698.1|AW348698
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|58022169|gb|CX708910.1|CX708910
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|298170111|gb|HO018735.1|HO018735
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|33388323|gb|CA851530.1|CA851530
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|15661937|gb|BI699308.1|BI699308
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|58022417|gb|CX709158.1|CX709158
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|33388305|gb|CA851512.1|CA851512
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|9258866|gb|BE347013.1|BE347013
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
EST: gi|151399436|gb|EV269307.1|EV269307
EST:     ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAG                         GTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA
genomic: ACTTCTTCAGCAATGTCTGTGAGCTTGATTTGGTTTTTAACTTCCACAAGgtttgttaat ... tgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactatttttttaatgtttccttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG
                    tccttac  putative branch site (score: 2)
     tatttttttaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcaccattaccatattgatcgtaccctcttcctttagattattattactatttttttaatgtttccttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG