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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

Basic information

species Glycine max
transcript GLYMA11G31450.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctc-tgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                          |  |||    |  | ||  |    |  |||||  |   | | |  | ||  | | ||  ||   |||||   | |||||  |||||        | |    | ||||||||||| ||||| |||||||| ||||| || ||||| ||||| || ||||| || || ||  | |||||||||||||| ||||| || ||  | ||  
----------------------------------------------------------------------------------------agggatttacacagatattgtcgagaa--tattttatgaaattcctatgcttgaaggttgaagtatttctcaccatgtgtttttttaa------aatgtcgaatgcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                       |   |    |   |  | |     || | |  |||   | || || | |||    |   | |   | ||   |  | |  |  | |  ||| || |  |      ||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||  | ||||||||| | || |||||||||||||||||||| || |||||  
---------------------------------------------------------------------------------------tctctaaaagcaaacttttggagttccaacagtttt-ctagattatagttcctactagctctttttgtttctt--attagtaatgttgttatctatgtta-----cagATGGATGGGTTTGATCAAACAGTGAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTCTGTTGCGTCCTGGTAGACTTGACA

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                        |   |      || || |     |     || ||   | || || | |||    |  ||||   ||||   |  | |  |  | |  |||  | |  |      ||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||  | ||||||||| | || |||||| ||||||||||||| || |||||  
----------------------------------------------------------------------------------------tctctaaaagctaactttgggaattcctatagtttcctagattataattcctactagttttttttatttctt--attagtaatgtggttatttatgttg-----cagATGGATGGGTTTGATCAAACAGTCAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTTTGTTGCGTCCTGGTAGACTTGACA

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 3
gtatctatgaaatgatatttctatta-ggtgctgtgagtatgttgttactacta--ttagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
|||  | | ||| |||||   | |||  | | | ||  | |  |   |  |      |   | | | |  ||      || |||     |  |     | || ||   ||   || | | |    |  || |||   ||||| | || |     | | | | | |  | |||| ||      ||    | |||| ||||||||||| |||||||| || || |||||||| || || |||||||||||  ||||||||||| |||||||||| ||  | ||||||||||| || || |
gtaggtttaaaaggatatggatcttatagagatatggatttaattaaaaaaaaggcctgaaaatcagttgttaactggggatgccaaaaaaaaagggct-ttgattaatttgtctgttgattacagcatgtact-tgcttctat-tgttagctaaaaatgtttaactttttggatttgg-gtctaaattcttctccagATGGATGGGTTTGACCAGACTGTGAATGTTAAGGTCATAATGGCAACTAATCGAGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACC

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                       || | |  | ||||||| || || |||  || | |   | |  |    ||   | || ||||   ||||  || || | ||  |||       || | |    | |||||||||||||| || |||||||||||||| || || |||||||| || ||  |||| || ||| | ||||| ||| |  |||| |||||| | || ||||
------------------------------------------------------------------------------------aattttgctcatttttatctttt-ccttct--ctctctctctcgtttttgttttgttttg-ttttgtttatttacttaactctttattt------ttgctatggg-tgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttctt-cagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                     ||| | ||  | | | | | |   |  |  | |  | ||   | | |        | ||       |  ||  | | | || | || |  |  ||  |  | | | | || || |||  | |  |  | ||  ||    |  |  ||  ||  |||     |  | |  || ||||||||||||||||| |||||||| ||||||||||| || ||||| || ||| | ||||| ||| | ||||| ||| ||||||| |||||| | |||||||
--------------------gtatgaagtctttttaatttctcagtttt-ttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacag--aactcggtagtcttcagttcatttttctcgtcgaagtttg--gctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                                                                                 |   ||  |     |  |||       | |   |||  | |  |  ||||||||||||||| || ||||| || ||||| || ||||| ||||| || ||| | || ||||||||||| || || || |||||||| ||||| |||||  
------------------------------------------------------------------------------------------------------------------------------------------------gtaaaaggaaccgagtagagtaagccgctgacgtcct--tgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                                                                                                                                                 |   ||  |     |  |||       | |   |||  | |  |  ||||||||||||||| || ||||| || ||||| || ||||| ||||| || ||| | || ||||||||||| || || || |||||||| ||||| |||||  
------------------------------------------------------------------------------------------------------------------------------------------------gtaaaaggaaccaagtagagtaagccgctgacgtcct--tgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

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|48575120|gb|CO036244.1|CO036244
EST:     GTACAGCGTATCCTTATGGAACTTTTGAATCAG                         ATGGATGGTTTTGACTAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: GTACAGCGTATCCTTATGGAACTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
EST: gi|208259637|gb|GE058029.1|GE058029
EST:     GGAACTTTTGAATCAG                         ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: GGAACTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
EST: gi|16284036|gb|BI945871.1|BI945871
EST:     CTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAG                         ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: CTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
EST: gi|48575128|gb|CO036248.1|CO036248
EST:     GTACAGCGTATCCTTATGGAACTTTTGAATCAG                         ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: GTACAGCGTATCCTTATGGAACTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
EST: gi|17152954|gb|BM142887.1|BM142887
EST:     CTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAG                         ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: CTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
                             gtttaat  putative branch site (score: 4)
                                   ttacctgttcttttct  CT-rich tract
     ttttagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG