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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGTGGGGTGTGTTGAAGGAGCATTGGGTATACGTGAGTGGCTGGAATCACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatattgcttacttaattcaagtttgagtaaactattattttggtctccaaaagtgtacaatgcaacaagttcttgaaactaggaaaatttcatt...

Basic information

species Glycine max
transcript GLYMA13G23790.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23790.4 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G049811_T01 (Zea mays), 5'ss of exon 2
TTCGTGGGGTGTGTTGAAGGAGCATTGGGTATACGTGAGTGGCTGGAATCACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatattgcttacttaattcaagtttgagtaaactatta-ttttggtctccaaaagtgtacaatgcaacaagttcttgaaactaggaaaatttcatt---
||||| || || || || || ||| | || || || |  ||||| || || ||||| ||||||||||||||||| |||||||| ||||| ||  | | |||| ||||    ||  |   ||  |             |    |          |||||     |       ||   |  || ||  ||||    || || |   
TTCGTCGGCTGCGTCGAGGGTGCACTCGGCATCCGCGGCTGGCTCGAGTCGCAGGGCCATCAGTACATTGTCACCGATGACAAGGAAGGCCCCAACTGTGgtcagta----gcccaggcaacccccccccccccccccccccaacacccacacccaaacaaagatttcagtacttctcatttaagttagggtggttccagtaat

upper sequence: GLYMA13G23790.4 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 5'ss of exon 2
TTCGTGGGGTGTGTTGAAGGAGCATTGGGTATACGTGAGTGGCTGGAATCACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatattgcttacttaattcaagt-ttgagtaaactattattttggtctccaaaagtgtacaatgcaacaagttcttgaaactaggaaaatttcatt
|| ||||| |||||||| ||||| ||||| || || || ||| |||||||||| || || ||||||||||| ||||||||||||||||| ||||||| |||||||||  | |  |    |  ||  || ||| || |   |      |   ||    |  ||     |||| ||| |  |  | ||    ||  | | |||
TTTGTGGGCTGTGTTGAGGGAGCCTTGGGCATTCGAGATTGGTTGGAATCACAAGGGCACCAGTACATTGTTACTGATGACAAAGAAGGGCCAGATTGTGgttagtacgtagtctttgaatgtcttgtgttgtgtgattcaaagagctt-cctatttacctgctagctgcatcaaataatacagacattaaagttgtgatt
















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|22523516|gb|BU082327.1|BU082327
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|5688024|gb|AI941039.1|AI941039
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|10233461|gb|BE802349.1|BE802349
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|17401013|gb|BM177795.1|BM177795
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|27426313|gb|CA937833.1|CA937833
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|11688957|gb|BF596695.1|BF596695
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|17400846|gb|BM177628.1|BM177628
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|213589062|gb|DB973162.1|DB973162
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|7233269|gb|AW568617.1|AW568617
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|17023857|gb|BM094891.1|BM094891
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|17023301|gb|BM094335.1|BM094335
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
EST: gi|6916468|gb|AW397998.1|AW397998
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTG                         AACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatat ... tctgctgcagAACTTGAGAAACACATTCCAGATGCCCATGTCATCATATCTACTCCATTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGTGGGGTGTGTTGAAGGAGCATTGGGTATACGTGAGTGGCTGGAATCACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCAGATTCTGgttagtatattgcttacttaattcaagtttgagtaaactattattttggtctccaaaagtgtacaatgcaacaagttcttgaaactaggaaaatttcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG