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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttctttttcattttcccttgtatgatttgagcaaagattccataaatatttattggtttgttactataatgttgtcacaagtctcaatattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG

Basic information

species Glycine max
transcript GLYMA15G02640.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 13
------gtcagttttctttttcatttt--------cccttgtatgatttgagc-aaagattccataaatatttattggtttg--ttactataat----gttgtcacaagtctca--atattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
      | |  |||||| |||    ||        |  || | |  || ||   ||   || ||   | ||| || |  | |   |  |  | |     ||||| |   |||||  | ||| | |  | |  |||||| | ||||   || ||||| ||||||||||| |||||||  ||| |  ||||||||||||| ||  | |||||||| |||| ||||||||| || || ||
gtatatgactattttctctttagacttaatagtgactattttctctttagacttaatagtttcagccacattcatggactaggactggtccagttctcattgtcccttttctcatcacattagctcatatgaaacagGTGGAGAAAATCCGGGAGTTGATGCTAATGGAAATTCTTACGATCTTTCAACAAAGTTGCTCCATCTTGCATGGCACCCAACTGAGAATTCCATCGCGTG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
gtcagttttctttttcattttcccttgtatgatttgagcaaagattccataaatatttattggtttgttactataatgttgtcacaagtctcaatattcgatattcttga-acagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
                             | | | |  || ||   |  ||||  ||  |     | ||||||   | |  ||   |||   ||  ||   | || | ||  ||||| ||||    || |||   || || ||||||||  | |  |||||||||||||||||||||||  | || ||||| ||||  ||||| |||||||||||
----------------------------gttagt-ggtcatagtacctgtaaaacttattcaagcttttactac--tctcttctggagtaaaaaacttt--tgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 15
gtcagttttctttttcattttcccttgtatgatttgagcaaagattccataaatatttattggtttgttactataatgttgtcacaagtctcaatattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
||| || |   | |   | |   || |  |  ||| ||||     |   |||| |   |||||  ||  | || |||               |||| |  |  || |  ||||||| ||||    || ||||| ||||  |||   ||| || |||||| |||||||||| |||||||  | || ||||||||||  ||||| |||||||||||
gtcggtatctctctctctatcatctcgc-tcgtttaagca-----ttattaaaaa---attggcatg--aatagaata--------------aatactgaaatttgtaaaacagGATCAGAGAGTCCGGGAGTCGATGGGAATACTAATGCTCTTGATTACACAACAAAGCTGCTGCATCTTGCTTGGCATCCAAACGAGAACTCAATTGCTTG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 13
gtcagt--tttctttttcattttcccttgtatgatttgagcaaagattccataaa------tatttattggtttgttactataatgttgtca-caagtctcaatattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
|| |||  |||||| |||  || |  |      |||  | | |  | |   ||||      | || |    | | || |   | |  |   | |   | || ||  | |  | ||    |||||||| ||   ||| ||||| ||||| ||||| ||||||||||||||||| ||||||||||| ||  |||||||||| |||||||| || ||||| || ||
gtgagtcttttcttgttctcttgctttctctctattcaaaccacaaatttttaaaatcgtcttttaagcaatattttcccccatttctcatatcctttttctattctggggaatccgtgacagGAGCCGATAGCCCAGGAGTTGATGCAAATGGAAATTCTTTTGATTTCACTACAAAGTTGCTACATCTAGCATGGCACCCAAGTGAAAACTCAATCGCCTG

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|7235075|gb|AW570465.1|AW570465
EST:     AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGG                         GAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
genomic: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGGgtcagttttc ... tcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
EST: gi|17519644|gb|BM188686.1|BM188686
EST:     AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGG                         GAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
genomic: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGGgtcagttttc ... tcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
EST: gi|26057605|gb|CA800519.1|CA800519
EST:     AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGG                         GAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
genomic: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGGgtcagttttc ... tcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgttactataatgttgtcacaagtctcaatattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
                                          tattctt  CT-rich tract
        ttactataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttttctttttcattttcccttgtatgatttgagcaaagattccataaatatttattggtttgttactataatgttgtcacaagtctcaatattcgatattcttgaacagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC