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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT

Basic information

species Glycine max
transcript GLYMA01G39950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 2
----------tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
          | |  ||| ||   ||||  | |   ||  |  | | |||   ||  ||||||       | |  ||||| | |||||||  || |||    |||||||||| || || || |||||||| ||||||||  | || || || ||||||||||| || ||||   ||||||||||||||||||| || |||||||| ||||
tttaacctcatatcttttcttccgaactgttctctgtttgctca-tgtgcttattagaattctc------tgtgctatta-tatatgagcagtttaattc--ttttgcagATAAAGAGGGAAATAAAAATTCTTCAGAACCTCTGTGGTGGTCCAAATATTGTCAAACTTCACAATATTGTCAGAGATCAACAATCAAAAACTCCAAGTT

upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 2
----tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
     || | ||||   |   || | | |     | || ||     |  || ||||   |||  |||   ||  |  |   |  | || | |    |||||||||| || || ||||||||||||||||||||  |||| ||||||||||||||||| ||||| |||||||||||||||||||| ||||| |||||||| || |
ttgcggtaaattttcccaggtttctatgggaattcttattac----tggcatattccattgacttttcagatatcagtgcaacatatttacttctgttttgcagATAAAGAGGGAGATAAAAATACTTCAGAACCTTTGTGGAGGCCCAAATATTGTGAAGCTGCTTGATATTGTCAGAGATCAGCATTCCAAAACTCCTAGCT

upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 2
tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttatta--ctttatgagctcttcaat--atcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
   || | |  |      ||   | ||| |   |   |    |   |||||| | | ||||  ||||| |  | |    |  |||| ||   ||  || ||||||| || || ||||||||||||||||||||  |||| || ||||||||| | || ||||| ||||||||||||||||| || ||||| |||||||| || |
---tagtctgatgttttatagcatttttgagaaatcgttgtgtagtaaattcat-taatatagtttatcagacatatccatttctttaaatgattgttgtgcagATAAAGAGGGAGATAAAAATACTTCAGAACCTTTGTGGGGGCCCAAATGTCGTCAAGCTGCTTGATATTGTCAGAGACCAGCATTCAAAAACTCCTAGCT

upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
--tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgc-agATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
  ||    |||   |    || ||  | ||  | | || | | |  | | | |  |||    | ||   ||| | |    |        |  ||  |||  ||||||||||||| || || |||||||||||| | || ||||| || ||||| || |||||  |||| ||||||||||| || || || || ||||||||| 
tatgacgatttggcagtgatttttccgctttgcattct-ttcgaactgatactaatct--cttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC

upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------tgttatttttttaaaacttattt-tgtttcacgtactatgccattt-------caaattcttctgatatt--ttttattactttatgagctct-----tcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
                                                                     | ||||  ||||   |   | |  |   |    | || |  ||        || || |  ||| | |  | || ||    | | | ||||     |   |     ||   ||||||||||||| || || ||| | |||||| | || |||||||| |||||||| |||||| | || |||||||||||||| || || ||||| |||||| 
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC

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|6454717|gb|AW185400.1|AW185400
EST:     GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAG                         ATTAACAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
genomic: GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAGgtactccttc ... cattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
EST: gi|192309673|gb|FK002911.1|FK002911
EST:     GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAG                         ATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
genomic: GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAGgtactccttc ... cattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
EST: gi|213608123|gb|DB972591.1|DB972591
EST:     GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAG                         ATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
genomic: GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAGgtactccttc ... cattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
EST: gi|213617929|gb|DB957382.1|DB957382
EST:     GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAG                         ATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
genomic: GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAGgtactccttc ... cattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
EST: gi|23725227|gb|BU760562.1|BU760562
EST:     GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAG                         ATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT
genomic: GCAATGAGCGCTGTATAATTAAGATTCTGAAACCTGTCAAGAAAAAGAAGgtactccttc ... cattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattcttctgatattttttattactttatgagctcttcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
       ttctgat  putative branch site (score: 3)
                                            tcatttt  putative PPT
       ttctgatattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttca