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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgcttttgttctttaaaccaatatttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG

Basic information

species Glycine max
transcript GLYMA19G36860.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 4
------------------------------------------gtatgcttttgttctttaaacca-atatttgattaccatggtttaataaaag---ctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
                                           ||  ||| |  | |  || ||  ||        ||| |    | ||  | |   || || |   || | |     | | |||   |    |      ||| ||||||||||||| || ||||| |||||||| ||||| ||||| |||||||||||||| ||||| || || || |||||||||||
gtaattttcttgttcccttgtttagttgctcttcaaatctcgatagacttgttatgtccaatcctcatgcccatagacctttcacttattgatgtccctagactcccgataaacctattacttac---tacagtttgggattatagGTTGGTCAAGAGCAGTTCTCGCCTAGTTCACCTGGCTGGCCTCCTTTCATGAGGGTCAATCCTATATTGGACTGGTCATACAG

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G381933_T03 (Zea mays), 3'ss of exon 4
----------------------------------gtatgcttttgttctt--taaac-caatatttgattaccatggtttaataaaagc--tggaatattgacatattat--attcatacgtgtgtgc---tcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
                                    |  |  |||  | |  |  || ||||  || ||  ||||||| |    |   |  |  | | |||  || | |   |    |  ||     |   |   |  | | |||||||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||||||||| || || ||||||||||||||
gtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgatt-atgcccatggtgttcccagttccttacagttttggtatctcactgaactttgagtaaacacaattttgaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATGAGGGTGAATCCAATCTTGGATTGGTCATACAG

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G028010_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------gtatgcttttgttctttaaaccaatat-ttgatt---accatggtttaa-----taaaagctggaatattgacatattatattcatacgtgtgtgctccta---ccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
                                                       ||  | | | |   |  | | | |||  || ||    ||||  |  ||     |    || ||  |  |||||| | ||  | ||    |||||     |    |||  ||||||||||| || | ||||||||||| |||||||  ||||| ||||||||||||||||| || || || |||||||| |||||
gtgactccccttgaattgagtgctcccgttttagtctacttcactgtcgtcattctacacctctatcgatctagctagtatactggttcatgccattctgcaacattttgggggccgggttcatgacatgtgatggtaattgcggtgtggaaaaaaatacttgtagGTTGGTCAACAAGAGTTCTCCCCTAGCTCGCCTGACTGGCCTCCTTTCATGAGGGTGAACCCTATCTTGGATTGGTCCTACAG

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149609_T01 (Zea mays), 3'ss of exon 4
gtatgcttttgttctttaaaccaatatttgattaccatggtttaataaaagct----------ggaatattgaca-tattatattcatacgtgtgtgctcctacc-ttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
||   |||   ||   |  |   |    ||  |  |||  |  ||| | |  |          ||   |||||   || | || ||    |||||       |    |  |||| |||||| || | ||||||||||| ||||| || ||||| ||||||||||||||||| || || || |||||||| |||||
gtg-acttcccttgaatcgaatgacgcctgcctgacataatcgaatgacaatttttttttgagggttcattgatggtaatctaatcgcg-gtgtgaatgaaaattgctgtagGTCGGTCAACAAGAGTTCTCCCCTAGCTCGCCCGGCTGGCCTCCTTTCATGAGGGTGAACCCAATCTTGGATTGGTCCTACAG

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcttttgttctttaaaccaata-tttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
||  ||||     ||| ||| |  || | | |  | |  | |  || | |   ||  ||| | | ||  |  |||  | | |   |||   |   || |||||||||||||| |||||||| |||||||| ||||| ||||| || || |||||||||||||| || || |||||||| |||||
gttagctt---cacttcaaatctttaatctcaagatccagatgcaa-atattttgtgatagtaaaatgattgattacttctta-atgcattt---tttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------gtatgcttttgttctt--taaacca------atatttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
                                          ||  |||   || |  || |  |      | ||||   ||  || |  | | || |     | |  | |    |  |||   ||  | | |     || ||| ||||| ||||||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||| || || || |||||||| |||||
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG

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|14258476|gb|BG881384.1|BG881384
EST:     AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGNGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
EST: gi|7691690|gb|AW759813.1|AW759813
EST:     AACCGATTCTAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCGTCTGGGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
EST: gi|7326913|gb|AW620711.1|AW620711
EST:     AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
EST: gi|192299088|gb|FG990402.1|FG990402
EST:     AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
EST: gi|193408937|gb|FK371597.1|FK371597
EST:     AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG
EST: gi|14260050|gb|BG882958.1|BG882958
EST:     AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCG                         GTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATG
genomic: AACCGATTCGAGCTATCTTCCTTGGAGTTCGAATTGGAGACCCTACTGCGgtatgtgaag ... taccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG
            tattgac  putative branch site (score: 2)
                                         ctcctacctt  putative PPT
          aatattgacatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttgttctttaaaccaatatttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG

gtatgct
- - - - - - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg