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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                              | ||   |    ||||     |    |   ||  |||  |   | ||||||    |   || |  |||||      ||  |  | || |    |      |||||||  ||||||||||||| || || |||||||| || |||||||| ||||||||| | |||||||||||||| ||||| |||||||| || |||||||| |
--------------------------------------------gctatta--ccagaaattgctgtttccct---attaatgtgaccta-ttgttttggaacaattgcgtattgtaaccatatggtttc-tgcttttctcaactgtttagATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattt--tttctcattgttcttgg-----attatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                                    |  ||    |  || || |   |||||    ||  | | || ||  | | | |  ||   ||   || | ||     |||   | ||  | ||||  |   || ||||||||||||||||||| || || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| || |||||  | ||||| || |
----------------------------------------------------gtctt----ttcgagtccttgagaatgt-cagagcagaattcttcgtagttctaattctgcaagattgtgggggcaaatttacaagttcttacttcctat-ttcagATATTGGAAATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                        |  ||||||     ||  || | |  |   |||      | || | |      ||        |      ||||   |||  ||    || |   |||| |||     ||||| |||||||||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| |||||||| || ||||| || |
----------------------------------------taagattttcatatttcaaagtttttaagatgtaaggaagctgcatacccaaggtggacgatatgggctccatta--cttatat----acatctcaactgttt-----tagATTTTGGAAATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcat---ttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                              ||      | |    |||   ||  |  |  ||  || | |        || || ||||| | ||   |||  |    ||   | ||     || |    |   |||||| |||||||||||||| || || |||||||| || |||||||| || |||||| | |||||||||||||| ||||| |||||||| || ||||| || |
----------------------------------------------ttccatattatttggtctttgtcaggcagggtgtctgtaca--------ttatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                             |  |||    ||     | | |  |     | |   |   |  || || ||| |||   | |  | || |   | ||||| |||  | || |    |    | |||||  | || ||||  ||||| || || || || |||||||| || ||||| ||||| ||||| || ||||||||||||||||| || ||||| || || |
--------------------------------------------ttccttgaatctttgccacagtagttcagacattt--taccatcaaatttttttttg---tgtaatgatggaattaggatt-tgatct-attatccgtgctttctagATTCTTGAGATGAGTCCAGAGGATGATGCAGAGGAAGATGGAGCGAATATCGATCTGGACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                   |||||         | |  ||   ||  |     || ||| ||   |   | | |||  |  ||  ||||  | | |   ||||   | | |   || |  |  |  |||  |||||| ||||| ||||| |||||||| || ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||||||| | || || ||||
-----------------------------------gtattcaa-----ctagttttcttatctta---tttttggtattt-tcctacagagtcttacct--atttgatttga--attct--aactgttgtgttaccatatcatgctattagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttct-cattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                                 | ||  |||     ||||     |  | || |    ||    | ||  |||| || |  || |||| || ||    | |    || | | | |||    |||||| ||||||||||||||||| || || || || ||||||||||| ||||||||||||||||| || ||||||||||| ||||||||  | || || ||||
------------------------------------------------ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgttt----ttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                            | | || |   | | | ||||     |    |   | | || |||    |   | | ||   |||||     ||| |||| | |  |||    ||||  |  |             | |  ||||||||||  | || |||||||| ||||||||||| |||||||| ||| ||||| | ||||| |||||||  ||||||||||| ||  | ||||| || |
-------------------------cgagaaagtagctctcgtgttttt---attccacagcttaattcctgttt--ttcgttgcaaccggttgtca---gatattttttaa--gtt----gatttcggtgc------------cctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA

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|6482551|gb|AW201806.1|AW201806
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|6915777|gb|AW397307.1|AW397307
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|298171738|gb|HO021330.1|HO021330
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|193703110|gb|FK639626.1|FK639626
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|298167852|gb|HO013115.1|HO013115
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|254339477|gb|GR848235.1|GR848235
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|4313874|gb|AI460993.1|AI460993
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|33390542|gb|CA853737.1|CA853737
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|298195561|gb|HO043952.1|HO043952
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|209719376|gb|BW674456.1|BW674456
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|120530681|gb|EH258814.1|EH258814
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|7924448|gb|AW830474.1|AW830474
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|27427306|gb|CA938826.1|CA938826
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|18040691|gb|BM308985.1|BM308985
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|213598762|gb|DB968233.1|DB968233
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|7042249|gb|AW472143.1|AW472143
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAG                         ATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacat ... ttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                   tgataac  putative branch site (score: 2)
                                         ctttttgc  CT-rich tract
                                     ataacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA