Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcattaagtttctatatcattattcattagcttagctttttgtgtctaagttctttctttcacttgatggaacactaattaattaattaatactaaaccatacttgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGTGAAGACTTTCCAGAACAAAACTACATTGTGAAGGAGGGTCAACTTGCAA

Basic information

species Glycine max
transcript GLYMA19G01200.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 5
gtattttcattaagtttctatatcattattcattagcttagctttttgtgtctaagttctttctttcacttgatggaacactaattaattaattaatactaaaccatacttgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGTGAAGACTTTCCAGAACAAAACTACATTGTGAAGGAGGGTCAACTTGCAA
      |    |||||||||      | ||| |   |||  |||   || | |  | | |||||    ||||       ||| || || |    |||     || |||    || | ||||| || || || ||||| || || |||||||| || ||| |||||||||| ||||||||||| | |||| | ||||| || |||||||| ||||| ||||
-----gtacccaagtttctac-----ttttcttctccttcccttcccgtatttttgct-tttctcatgcttgta-----actcataaaatggccaatg--ggacaata----ttgtgcagTTGCGATACGCAGCTGGAGTGAAGGACATGCTAGACAGGTACTTCAAGGGAGAAGACTTTCCGGCACAACATTACATCGTCAAGGAGGGCCAACTAGCAA
















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|58017267|gb|CX704009.1|CX704009
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|33389257|gb|CA852464.1|CA852464
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|192317369|gb|FK011706.1|FK011706
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|7145963|gb|AW507885.1|AW507885
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGTACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|22521954|gb|BU080765.1|BU080765
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|19934596|gb|BQ079626.1|BQ079626
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|58024603|gb|CX711344.1|CX711344
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|192320824|gb|FK013914.1|FK013914
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|37996280|gb|CF807869.1|CF807869
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|9259484|gb|BE347639.1|BE347639
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|192327787|gb|FK022066.1|FK022066
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|254315424|gb|GR825233.1|GR825233
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|57576050|gb|CX549021.1|CX549021
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|192320825|gb|FK013915.1|FK013915
EST:     CATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|4300722|gb|AI443088.1|AI443088
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|254315423|gb|GR825232.1|GR825232
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|6848238|gb|AW350528.1|AW350528
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAG                         TTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcat ... tgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgatggaacactaattaattaattaatactaaaccatacttgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGTGAAGACTTTCCAGAACAAAACTACATTGTGAAGGAGGGTCAACTTGCAA
                               tactaaa  putative branch site (score: 1)
                                           cttgtttttc  putative PPT
                taattaattaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcattaagtttctatatcattattcattagcttagctttttgtgtctaagttctttctttcacttgatggaacactaattaattaattaatactaaaccatacttgtttttcagTTACGTTATGCTGCTGGTGTCAAAGACATGCTTGATAGGCACTTCAAGGGTGAAGACTTTCCAGAACAAAACTACATTGTGAAGGAGGGTCAACTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG