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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccttgcccaaagtaattttcttcatttcccgaaatggaatgttttgcttaattttcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG

Basic information

species Glycine max
transcript GLYMA12G04460.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 3
gtgtgccttgcccaaagtaattttcttcatttcccgaaatggaatgttttgcttaattttcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
  ||   |   ||  | || ||  | ||||||    ||    |      |||  |  |        |||   |  || | || |  || || || ||||||||||  ||||| ||||| | ||||||||| |||||| |||| |||||  |||||||||||||||  ||||| || || ||| | |||
--gtatatataccctattacttaccatcatttttttaacccaa-----ctgcaaacatgctgatgacttgactaattgatttgtgtagATTTCTAAAAGCAAGGAGATTTGACATTGAGAAAGCAAAGCAAATGTGGACTGACATGCTTAAATGGAGGAAGGAGTACGGTACAGATACAATTGTTGAG

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g50616.1 (Oryza sativa), 3'ss of exon 2
------------------------gtgtgccttgcccaaagtaattttcttcatttcccgaaatggaatgtt--ttgcttaatttt---cttcttcttatttt-------ttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                        ||     || |    | |  |  |      | |   ||||  |  |||  ||  || ||||     |||||| | |          | ||||   |  ||||||||||||||  | || ||||||||||| | |||||| ||||||||| | || |||||   ||||||||||||||| ||  ||||||  ||   |   
gtgcaatttttttctgatctcagagtcacagttacttggatttctccttactcctgcagaaaattcagcgttgcttatttgatttaaaatttcttcatgtgcctatgacatgttacacatgtagGTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG---

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtgtgccttgcccaaagtaattttcttcatt-------tcccgaaatggaatgtt------ttgcttaattt---tcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                                                        || |   || ||   |  |  ||| | |||          |   ||| |||| |       ||  ||  |||   | |||||  |||   |||||| | ||  |||||||||||||||| || ||| ||||||| | |||||| ||||||||| | || |||||   |||||||||||| |||||| |||||| |||   |   
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgta--gGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 3
------------------------------gtgtgccttgcccaaagtaattttcttcatttcccgaaatggaatgttttgcttaattttcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                               | ||  | ||   | ||  |  | |||||||  | ||||   | ||   ||  |  |     ||   ||  | |  |  ||    || || || ||||||||||| |||||||| || | ||||||||| ||||||   |||||||| || ||| ||| ||||| ||| ||||| || ||| |||||
gtatatgtatccagtaaattatgatgcaccttttgtttagcttgatgtgttagttttcatttttccaaatcacaagt---gcacagctcaagcctaactaaatctggtcttt----agATTTCTAAAAGCAAGGAAATTTGATATCGACAAAGCAAAGCAAATGTGGATGGATATGCTTCATTGGCGGAGGGAGTATGGCACTGATACGATTTTGGAG

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgccttgcccaaagtaattttcttcat------ttcccgaaatggaatgttt----tgcttaattttcttcttcttattttttttacttt---tacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
 | |    ||  | || || ||||  | ||      || |   ||     | ||     ||  ||  | |    || |||      |||  ||   | ||||||| ||||||||||||||||||||||||| | ||||||||| |||||| |||||||| | || ||||||||||| |||||| ||||||| ||| |||||
-tattttatgttccaactattttttattatatggtattgcttcaactatgttttcataatgagtaggtataacattgttaagagcattatattacttgcagGTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGGAG

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|208156833|gb|GD956303.1|GD956303
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGC
EST: gi|193710828|gb|FK644683.1|FK644683
EST:     ATGGAGGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|208034208|gb|GD837632.1|GD837632
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGCATATGTGGG
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGG
EST: gi|193512335|gb|FK468217.1|FK468217
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|151397966|gb|EV267839.1|EV267839
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|14259642|gb|BG882550.1|BG882550
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|193685314|gb|FK625788.1|FK625788
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCTTGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|193583563|gb|FK541059.1|FK541059
EST:     ATGGAGGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|208239380|gb|GE041252.1|GE041252
EST:     ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGGGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAAAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... acttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgaaatggaatgttttgcttaattttcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                 gcttaat  putative branch site (score: 4)
             ttttgcttaattttct  CT-rich tract
                   ttaattttcttcttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccttgcccaaagtaattttcttcatttcccgaaatggaatgttttgcttaattttcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG