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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttatactaagatatatatcattatatttttttctttaatttgtaaggcattcttcgatatgttttgaagttgtttctgtatgtatatgatt...

Basic information

species Glycine max
transcript GLYMA14G02530.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02530.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g31040.1 (Oryza sativa), 5'ss of exon 11
AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttatactaagatatatatcatta-tatttttttctttaatttgtaaggcattcttcgatatgttttgaagttgtttctgtatgtatatgatt
  |    || ||  |  | ||||| ||||| ||  |||| || ||||||||||||||||||||||||||| | ||||| ||||| || ||  |||| |||||            || |  | | | |  ||  |   || |  |||  ||||||||     ||   | | |      || | | |||  |||||       
GGCACAGTCCATCAACAATATGGCAGGAGGGACCTTTACCATCTCAAATGGTGGTGTTTATGGAAGCCTTATCAGTACACCTATCATTAATTCTCCACAGgt-----------gctcacttgtttttttttgctgccttgtaattttgtttgtaagtt-ccctctaacacg------agctttatcta-atgtag------

upper sequence: GLYMA14G02530.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 12
AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttatactaagatatatatcattatatttttttctttaatttgtaaggcattcttcgatatgttttgaagttgtttctgtatgtatatgatt
  |  | ||||||||||||||||| ||||| ||  | || || || || ||||||||||| ||||||||| | || || ||||| |||||||| || |||||          |  |   |  |  |  |    |||    ||  ||  |||  |  ||||| ||   |     || |  | | |||  ||| |       
GGCACTCTCAATTGATGAGATGGCAGGAGGAACATTCACCATCTCTAACGGTGGTGTTTACGGAAGCCTTATCAGCACACCTATCATCAACCCCCCACAGgtcctttttcatttttgccacttgcaaaa----attgccctcactaggttgatattcattcatctg-acacaatgtatatatatcta-atgcag------

upper sequence: GLYMA14G02530.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 14
AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttatactaagatatatatcattatatttttttctttaatttgtaaggcattcttcgatatgttttgaagttgtttctgtatgtatatgatt-----
|||  ||||||| ||||||||||| |||||  |  | ||| |||||||||||||||| |||||||| ||| | || || ||||| |||||||||||||||||| |          |  |||   |   ||  ||        |  ||   | ||||  || ||   | |||||   | |  |     ||  | ||| ||      
AACCATATCAATCGATGAGATGGCAGGAGGATCATTCACAGTATCAAATGGTGGTGTCTATGGAAGTCTTATAAGCACTCCTATCATCAACCCTCCTCAGgttcga---------ttcgatccttgcaatactaaaaaccaatcaaa---gaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtag

upper sequence: GLYMA14G02530.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 5'ss of exon 8
AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttgg-aagttatactaagatatatatcatta-tatttttttctttaatttgtaaggcattct--tcgatatgttttgaagttgtttctgtatgtatatgatt
 |   || | |||||||| ||||| ||||| ||| |||| || || ||||||||||||||||| || ||  | || || |||||||||||||||||||| ||| |  || || |     || |  | |  | | |||  | || ||  | ||    ||||       ||| |||        || |||| | |  |  | |   
GAGCATAACCATTGATGATATGGCGGGAGGAACTTTTACTATCTCTAATGGTGGTGTTTATGGGAGTCTCATAAGCACTCCTATTATCAACCCTCCTCAAgttggtcaatttctttctcgacaactcttttgaatatcctcttgttataattaactggcagcgaaaccgaaatgcaa-atgtttatttccgaaattccagg---

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|209725638|gb|BW663127.1|BW663127
EST:     CAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: CAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|58018648|gb|CX705390.1|CX705390
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|209710456|gb|BW657328.1|BW657328
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|15589596|gb|BI674212.1|BI674212
EST:     GCGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACG
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACG
EST: gi|16283623|gb|BI945649.1|BI945649
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|209703724|gb|BW670687.1|BW670687
EST:     GTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|21256004|gb|BQ452892.1|BQ452892
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGTA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|192309689|gb|FG999902.1|FG999902
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|15589589|gb|BI674205.1|BI674205
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|19269269|gb|BM885525.1|BM885525
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|6725931|gb|AW310330.1|AW310330
EST:     GTGGTGTTTATGGCAGCCTTTTGAGTACCCGTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|209712272|gb|BW668466.1|BW668466
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|192309688|gb|FG999901.1|FG999901
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... tttttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCAAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttatactaagatatatatcattatatttttttctttaatttgtaaggcattcttcgatatgttttgaagttgtttctgtatgtatatgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC