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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtagaaatgtgaataattgctggaaattttaaataattttag...

Basic information

species Glycine max
transcript GLYMA02G09090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 2
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagt--tggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtagaaatgtgaataattgctggaaattttaaataattttag--
|| || ||||| ||| | || ||||||||||| |||||||| || ||| | || ||||| || || || ||||||||||| |||||||||||| | ||||||  |   | |  |   |  |  || |      | | |  ||   ||||    ||| || || |||      |  |    |   || | | ||  | |  
GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttttgaccttttgtt--gcaaattttgtgatcagtacttttgaaagtc--atgctataattgttttggttaaccctgaccattgattgatgatggaa

upper sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G76860.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttggaatcagtaactaagag--aaatacacatttattttttggcaaagcttaatg-gtagaaatgtgaataattgctggaaattttaaataattttag
|| | |||||||||| | ||||||||||| || |||||||||||||  || |||||||| ||||||||||| |||||||| ||||| |||||  ||||| ||     |   ||   || ||  || |  | |  |||||   ||   | ||| ||| ||    || | |  | ||   |  | | ||| | ||     |
GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGGgtacgtgctttttcttactcaatagttaactttataggtatttga-gggggatcttgatgagtttctatctca--agttaaggatattgttagagaacaagtg

upper sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G21190.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtag---aaatgtgaataattgctggaaattttaaataattttag---
|||| |||||||||| | ||||||||||| || |||||||||||  | ||||| ||  | |||||||| || |||||||| ||||| |||||  ||||| ||     ||  || || |   | ||  |   ||| | | ||  |    ||| | |||    ||| ||   |   | |   | |||| |  || |   ||   
GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctct-tagctcaataagattta---ttaatctatg-taggctttagtagtaagataaacgtttttgggttcaaaatatttcagcta-tcacagtat

upper sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 5'ss of exon 2
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgg-aatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtagaaatgtgaataatt-gctggaaattttaaataattttag------------------------------------------------------------------------------------------
|| |||||||||||| | || ||||||||||| ||||||||||||||  |||||||||| |||||||| ||||| || || |||||||||||  | ||| | |   ||   |   |             | |  ||| | |||    |   ||  | |  |||    |  ||   |||| |  |  | |||| |  |                                                                                           
GCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGAgtatgctctcaactggcttccttttacttctttcttaaattatctggtttggtagaactgaaacaatccagaagatccactggca--taaacataactgcaccaccacaagccccaatcccccaccctgctgagaggaattaaataaataagcataacaagaatgtttctggaatttttttttttttgatag

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|31470689|gb|CD412717.1|CD412717
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGTTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192305412|gb|FG994262.1|FG994262
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|298190498|gb|HO032619.1|HO032619
EST:     TCATTACTACAGTGGAAATCGACGATGAGACACACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|207749958|gb|GD719108.1|GD719108
EST:     TTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         AACTACAAAGCGGACAGTT
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagA-CTACAAAGCGGACAGTT
EST: gi|192297747|gb|FG989608.1|FG989608
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|7588632|gb|AW704423.1|AW704423
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192305383|gb|FG994261.1|FG994261
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192334624|gb|FK025857.1|FK025857
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|7686196|gb|AW756844.1|AW756844
EST:     TTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|8827162|gb|BE210892.1|BE210892
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192329676|gb|FK022942.1|FK022942
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ATTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|207778525|gb|GD750572.1|GD750572
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192326439|gb|FK017711.1|FK017711
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192329675|gb|FK022941.1|FK022941
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|192324193|gb|FK017924.1|FK017924
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|193633212|gb|FK578808.1|FK578808
EST:     TTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGT
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGT
EST: gi|24135733|gb|BU926243.1|BU926243
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|151402513|gb|EV272326.1|EV272326
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|31476082|gb|CD418110.1|CD418110
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|18040528|gb|BM308822.1|BM308822
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|193425577|gb|FK386890.1|FK386890
EST:     TTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTACCTGTTTGTCAGGG
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTT-CCTGTTTGTCAGGG
EST: gi|208306259|gb|GE104408.1|GE104408
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
EST: gi|151406944|gb|EV276759.1|EV276759
EST:     TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG                         ACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA
genomic: TCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgga ... ttgattgcagACTACAAAGCGGACAGTTCCTTTCCTGTTTGTCAGGGGAGATGGGGTGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtagaaatgtgaataattgctggaaattttaaataattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaaa