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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT

Basic information

species Glycine max
transcript GLYMA13G31130.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 1
-------------------gtttgttg---tcctctgaaaccctac---ttttgctttctgcttcgatttcttgccattggga-----ctaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
                     ||| ||    || | ||    |||    ||||    |  | || ||||| ||     ||||      || |||      |    |  |||| ||| ||||||||||| ||||| || |||||||| || ||||||||||| ||||||||||| |||| ||||||
gtaagacgctcctcgtcgccgttgctggatcccccagatgagctagggattttatggtagggttagatttttttttcgtgggtggcttctgattcgtgtggtttccgccttcgttttcagTTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 1
--------------------------------gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgt--ccgcac--acaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
                                    || ||| |||  | ||    |   |||   || |||  | |   ||  || |  || ||| |||   ||| |  |  |  | ||  |||||||||||| || || || |||||||| || ||||||||||| ||||||||||| |||| ||||||
gtacccatttctcctcctcccctccccgcgggcgacgtggtcgtctcgatcc--ggtccggctggttgtttct-tgtagcgcggtttgatctgattttgtggtcgccctgatgatgttttgcgcagTTCAACATCGCCAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattg-ggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
                 |  |||||   |  || | |  ||||     |   ||| ||    ||  | || |  |    |    ||| ||||||||||| ||||| ||  ||||||| || || ||||||||||| |||||||| |||| ||||||
---------------gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaatta-tgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
                 |  |||||   |   | | |  ||||     |   ||| |   |  || | || |  |    |    ||| ||||||||||| ||||| ||  ||||||| || || ||||||||||| |||||||| |||| ||||||
---------------gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T03 (Zea mays), 3'ss of exon 1
-----gtttgttgtc-ctctgaaacc---ctacttttgctttctgcttcgatttcttgccattgggactaatta-tgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
            | | |  ||||      |||||   |   | | |  ||||     |   ||| |   |  || | || |  |    |    ||| ||||||||||| ||||| ||  ||||||| || || ||||||||||| |||||||| |||| ||||||
gcgcgccgcaacgccaccatgaaggtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 1
gtttg-ttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
||  | || ||||| |   |  ||   | | |   || |    ||| | |  ||   |  |  | || |  || |    | |   || ||||||||||| ||||| ||  | ||||| || |||||||||||||| |||||||| |||| ||| ||
gtaagcttatcctccgcg-ctgtaacatcgataggtggt---gtttgtgggaatctagcgtc-tgatctgtgcccttttcgttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
||  ||         |     ||   |     | |||| ||  |||  |         ||||   | | |  |     |||| ||| ||||||||| |||||||||| || || || || ||||||||||| |||||||| ||||||| ||| ||
gtgcgtgacggcgaaatcgaatagactctacatttgct-cgtattcgagtttcctttgctaacctttttc--atgtttcttcgttt-cagTTCAACGTTGCGAATCCAACTACTGGATGCCAGAAGAAGCTCGAGATCGACGATGACCAGAAACT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 1
---gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
   | |   | |  |      |   | || ||  ||||  ||    |  |||  |||  |  | |||     ||        || | | |||||||||| | || ||||| |||||||| ||||| ||||| || ||||||||||| || |  || ||
gtggctccatctttttcttctcatcaattctg--ttctcgtttatctctttgttatttcgtttgatt-caatcgattttggtttgtgtcgcagTTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACT

upper sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
gtttgttgtcctctgaaaccctacttttgctttctg--cttcgatttcttgccattgggactaa---ttatgtccgcacacaacttct--tttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
     | |  |   |||| || | ||    ||  ||  || ||     |   || ||   | ||    ||  |    |  |    | |  |||||||||||| || |||||||| ||||| || || ||||||||||| ||||| || ||||||| ||| ||
---gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT

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|208176390|gb|GD978597.1|GD978597
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|298182669|gb|HO031404.1|HO031404
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|193708153|gb|FK642459.1|FK642459
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|151407299|gb|EV277114.1|EV277114
EST:     AGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: AGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|41145367|gb|CK605578.1|CK605578
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTACGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|11413313|gb|BF425324.1|BF425324
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|298173823|gb|HO017159.1|HO017159
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTCGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|151403312|gb|EV273122.1|EV273122
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|298175030|gb|HO018025.1|HO018025
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|298181172|gb|HO022611.1|HO022611
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|298190922|gb|HO038401.1|HO038401
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|17519909|gb|BM188951.1|BM188951
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|18040763|gb|BM309057.1|BM309057
EST:     GAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|8283060|gb|BE020621.1|BE020621
EST:     GGAGGCGAACAGAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|10846367|gb|BF071320.1|BF071320
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|192326806|gb|FK018558.1|FK018558
EST:     GGAGGCGAACAAAGAAACTCAGAGACCCGAGGGCAGATTTCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: GGAGGCGAACAAAGAAACTCAGAGACCCGAAGGCAGATTTCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
EST: gi|17400921|gb|BM177703.1|BM177703
EST:     TCAAGATGAAG                         TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT
genomic: TCAAGATGAAGgtttgttgtc ... tcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
                     gactaat  putative branch site (score: 2)
                                           cttcttttgc  putative PPT
                      actaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC