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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactccttcttatgacttcttatatacttctgctgtttcttggagcctttcattccgttggatgttctattactttttcttttgctctatttttttttataacagatattgagatggtcttcatgcccttttctcaaacagcttcctcttattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATTTTAAGCGAAGAGCAAGAGAATGAACTTCCTAACTTCCCATCATTCATTC

Basic information

species Glycine max
transcript GLYMA09G36770.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 2
gtcactccttcttatgacttcttatatacttctgctgtttcttggagcctttcattccgttggatgttctattact--ttttcttttgctctatttttttttataacagatattgagatggtcttcatgcccttttctcaaacagcttcctctta-ttttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATTTTAAGCGAAGAGCAAGAGAATGAACTTCCTAACTTCCCATCATTCATTC
                                                     |||  | |  |||    | | ||  ||  |  | | |||| | ||||      |  || |||   |||| |     | |  |||| | || | |   ||||| ||||||||||||||||||| ||||||||||||||||||||||  ||||||||||||||| |||  ||||| ||||| ||||||||||| || || |||||||||||||
-----------------------------------------------------attggggtttatgaatgaatgctagttgcccatggttctactcttttccc---ctaattttg---tggtat-----cacaattctgatactgatgtttcttaattttgtagGTTCGCAGGCTGAGGATACAACAAAGAATTAAAAGTGCTGAACTTGGAATTCTAAAAGAAGAACAAGAAAATGAACTTCCAAATTTTCCATCATTCATTC

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 1
gtcactccttcttatgacttcttatatacttctgctgtttcttggagcctttcattccgttggatgttctattactttttcttttgctctatttttttttataacagatattgagatggtcttcatgccctt----ttctcaaacagcttcctctta--ttttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATTTTAAGCGAAGAGCAAGAGAATGAACTTCCTAACTTCCCATCATTCATTC---
                                                                  |||| || |||| || ||    |      |  |   ||   ||  | |  |||  ||  || | |     |||| | || | ||  |||||  ||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||| |||   |||| || || |||||||| |  || || |||||||||||||   
------------------------------------------------------------------ttcttttgctttatcattaaagcacagaatgctgtcaatctatgcttat-tggggtttgtggcatcataattcttatactggtttttcttaatttttgtagGTTCGCAGGCTGAGGATACAACAAAGAATTAAAAATGCTGAACTTGGAATTCTAA---AAGAACAGGAAAATGAACTCCAAAATTTTCCATCATTCATTCCAT
















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|23057217|gb|BU577892.1|BU577892
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|4300666|gb|AI443080.1|AI443080
EST:     GGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATTGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTTGAAT
genomic: GGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACAT-GGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAAT
EST: gi|9987763|gb|BE661871.1|BE661871
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|193519696|gb|FK477141.1|FK477141
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAACTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|298165597|gb|HO011646.1|HO011646
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|19270747|gb|BM887003.1|BM887003
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|15813355|gb|BI785630.1|BI785630
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACTTGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|13791409|gb|BG654000.1|BG654000
EST:     ATGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCATTCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|298195324|gb|HO039155.1|HO039155
EST:     ATGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCATGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|298181545|gb|HO025720.1|HO025720
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|27424921|gb|CA936441.1|CA936441
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|298164288|gb|HO013933.1|HO013933
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|5753292|gb|AI960579.1|AI960579
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|254342695|gb|GR858857.1|GR858857
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|21285677|gb|BQ473548.1|BQ473548
EST:     CAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: CAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|15336929|gb|BI497585.1|BI497585
EST:     AAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
EST: gi|151400607|gb|EV270421.1|EV270421
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtcactcctt ... tattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattgagatggtcttcatgcccttttctcaaacagcttcctcttattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATTTTAAGCGAAGAGCAAGAGAATGAACTTCCTAACTTCCCATCATTCATTC
                                     cttcctcttattttgt  CT-rich tract
                                            ttattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactccttcttatgacttcttatatacttctgctgtttcttggagcctttcattccgttggatgttctattactttttcttttgctctatttttttttataacagatattgagatggtcttcatgcccttttctcaaacagcttcctcttattttgtagGTTCGCAGGCTTAGGATACAACAAAGAATTAAAAACGCTGAACTTGGAATTTTAAGCGAAGAGCAAGAGAATGAACTTCCTAACTTCCCATCATTCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA