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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattg--attatgacgtgataattttttgca----tttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                                    || |||   | |||  | |||   |      |  || ||    | ||| |||  ||  |||    ||||  |  ||   ||      ||||  ||    |||||||  ||||||||||||| || || |||||||| || |||||||| ||||||||| | |||||||||||||| ||||| |||||||| || |||||||| |
---------------------------------------------------gctatta--ccagaaattgctg---tttccctattaatgtgacctattgttttggaacaattgcgtattgtaaccatatggtttctgcttttctcaactgtttagATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtt----tcttgatttttaaacatttttcattgattatgacgtgataattttttgcattt-agATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                                        |  ||  || || |   |||||   |   | || |  |     |  | ||| |  || ||| |      |   | ||  | |  |  ||   |||| ||||||||||||||||||| || || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| || |||||  | ||||| || |
-------------------------------------------------------gtcttttcgagtccttgagaatgtcagagcagaattcttcgtagttctaattctgcaagattgtgggggcaaatttacaagttcttacttcctatttcagATATTGGAAATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggactttta-attctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatg-acgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                               |  || ||| | |||   ||  || |   ||| | ||||      |       |      | |     | ||||  ||||  || |   || | |||     ||||| |||||||||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| |||||||| || ||||| || |
-----------------------------------------------taagattttcatatttcaaagtttttaagatgtaaggaagctgcatacccaaggtggacgatatgggctccattacttatatacatctcaactgttt-----tagATTTTGGAAATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                             ||    | | ||   |||   ||     |  ||  || | |  | || |||     ||| |       |   ||  |   || | |  |   |       ||||||| |||||||||||||| || || |||||||| || |||||||| || |||||| | |||||||||||||| ||||| |||||||| || ||||| || |
---------------------------------------------ttccatattatttggtctttgtcaggcagggtgtctgtacattatttatttt---gtttctgggttactcatatacagcctgccttttt--ctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                            |  ||| |  |||    |  | |  |   ||     |   |  || || ||| |||   | |||  ||        |||| |||  | || ||   |    | |||||  | || ||||  || || || || || || |||||||| || ||||| ||||| ||||| || ||||||||||||||||| || ||||| || || |
-------------------------------------------ttccttgaatctttgccac--agtagttcagacattttaccatcaaatttttttttg---tgtaatgatggaattaggatt-tgatct-attatccgtgctttctagATTCTTGAGATGAGTCCAGAGGATGATGCAGAGGAAGATGGAGCGAATATCGATCTGGACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                   |||||        | |  || | ||  |  || ||  | | |       | |   ||   | ||   ||| ||      |||  | | | |   || |  || |  |||  |||||| ||||| ||||| || ||||| || ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||||||| | || || ||||
-----------------------------------gtattcaa----ctagttttcttatctt--atttttggtattttcctacagagtcttacctatttgatttgaa------ttc--taactgttgtgttaccatatcatgctattagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaa-acatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                                                | |   ||      ||||    ||  | || |    ||    | ||  |||| || | |  ||||||||  ||   | |    || | | | |||    |||||| |||||||||||||| || || || || || ||||||||||| ||||||||||||||||| || ||||||||||| ||||||||  | || || ||||
-----------------------------------------------ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgttt----ttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                            | |  | |   | |  |||||    ||  |   || ||| | |||   |   | | ||   |||||    |  |||||||          ||||||  |  |             | |  ||||||||||  | || || ||||| ||||||||||| |||||||| ||| ||||| | ||||| |||||||  ||||||||||| ||  | ||||| || |
-------------------------cgagaaagtagctctcgtgttttta---ttccacagcttaat-tcctgtttttcgttgcaaccggttgtcagatattttttaag---------ttgatttcggtgc------------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|6566718|gb|AW234350.1|AW234350
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|207832509|gb|GD804823.1|GD804823
EST:     TAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: TAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|209727224|gb|BW663197.1|BW663197
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAACATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|192298921|gb|FG987666.1|FG987666
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|192294338|gb|FG987267.1|FG987267
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|192317513|gb|FK008965.1|FK008965
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGATGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|209718510|gb|BW662655.1|BW662655
EST:     AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: AGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
EST: gi|207770236|gb|GD740968.1|GD740968
EST:     TAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAG                         ATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT
genomic: TAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatat ... ttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA
                     cattgat  putative branch site (score: 4)
                                         ttttttgc  putative PPT
     atttttaaacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

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