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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataagacagattgtctcaataaactaattcttctgttattattgggtagttataattcttttccagaatattctctaattcttacagtcacatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC

Basic information

species Glycine max
transcript GLYMA18G49770.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49770.2 (Glycine max), 3'ss of exon 10
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 10
-----------tataagacaga-ttgtctcaataaactaattcttctgttattattgggtagttataattcttttccagaatattctctaattcttacagtcacatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC
            |||    | |    |||  | ||  | |  |  ||||| |    |   | |||||     ||||     |    | | ||| | |          ||||||| |||||| |||||||||| |||||  |||| ||| | || || ||  | ||||| |||||||| |||||||||||||| || || || ||| || |||
accagctaggacatagactaaaaccttctttagaacttgaaccaactgttttcgaagaacaattata--cactttctgagttcacttttgattttga----------aacagCTATACAAAGCCCGGGAAGAGAAGTACTTGCTGGATATACAGAGAGTTAACGGTCCGCAGTTTCTCTTCTTGGATCTATGCGCCGCCTTTCTTACAGAGC

upper sequence: GLYMA18G49770.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
tataagacagattgtctcaataaactaattcttctgttattattgggtagttataattcttttccagaatattctctaattctt-acagtcacatc-aacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC
  || | |  | |    | ||    |   |||| | | ||||||    || |     | ||    ||||  | | |||| ||||  | |  |   | |||||||||||||||| || || || ||||||||||||||||| || || || ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||
--tatggctaaatcatactattgcttgtgtcttatataattatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
















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|120491548|gb|EH219715.1|EH219715
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|254324882|gb|GR834307.1|GR834307
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|22930172|gb|BU547311.1|BU547311
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|193697101|gb|FK635359.1|FK635359
EST:     ACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: ACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|254336680|gb|GR842859.1|GR842859
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|120491873|gb|EH220040.1|EH220040
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|254315448|gb|GR825257.1|GR825257
EST:     TGAGAATGATGCTGTTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAAGTATCTGCTTGATCTTCAAAGGGTGCA
genomic: TGAGAATGATGCTG-TTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAG-AAAAGTATCTGCTTGATCTTCAAAGGGTGCA
EST: gi|192300226|gb|FG989348.1|FG989348
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|14991984|gb|BI317657.1|BI317657
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|254322930|gb|GR835645.1|GR835645
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|21675558|gb|BQ627909.1|BQ627909
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|209717386|gb|BW659062.1|BW659062
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|120491804|gb|EH219971.1|EH219971
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|58016406|gb|CX703148.1|CX703148
EST:     TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
genomic: TTGAGAATGATGCTGTTTCTACTTCAAATGTGGTCAAGTTTGAAGTGCAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAG
EST: gi|58022887|gb|CX709628.1|CX709628
EST:     GTGGTCAAGTTGGAAGTGCCAG                         CTTTACAAAACCCGGGAAGAAAAGTATTTGCTTGATCTTCAAAGGGTGCA
genomic: GTGGTCAAGTTTGAAGTG-CAGgtaatttacc ... acatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtagttataattcttttccagaatattctctaattcttacagtcacatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC
                                  ttcttac  putative branch site (score: 2)
     ttataattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataagacagattgtctcaataaactaattcttctgttattattgggtagttataattcttttccagaatattctctaattcttacagtcacatcaacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT