Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC

Basic information

species Glycine max
transcript GLYMA03G34890.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
||||||  |  ||   | |||   | ||  || |  ||  |||  ||||| |   | |  |  || |   || |   ||  |     | |||||||    ||||||||||||||| ||||||||| | || ||||||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||||||   |||||||
gtaagttcatatt---accgttacttttatttgttgatttttt--ttcagcta--aatcgtgctagt---aagtgctttcgatgtaatattctcta----gCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 13
gtaagtatactttcaaaacgt--gtatcttccttttgaatc---gtttgattcaga-tgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
|||||||   |||| |  | |  | |  |  |  || ||||    ||| ||| | | | | |||  | || | ||  ||   |||    | |  |||   || |||||| || |||||||| || ||||| || || ||||| |||||||||||||| || ||||| ||||| |||||||| ||| | ||||| ||    ||| |||
gtaagtaccatttccattcttcagaagttcacccttcaatccctttttcattgaaaatattattcatctt-tggcttatcttgttctttttccatttaaata-ttagCCCGAATGGATGGCACCTGAAGTGCTCCGAGATGAACCATCCAATGAGAAATCTGATGTCTACAGTTTTGGTGTAATCCTATGGGAACTTATGACAATGC

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttct-ctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
              ||    | |   | | ||| |  |  |||| ||       || || |||  | ||    |||||   | ||  |    | |||  ||||||||||||||||| ||||||||||| || || ||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||||||    |||||||
------------gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctat-gtggc----taagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G036902_T01 (Zea mays), 3'ss of exon 1
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttctctac-ttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
                     |||    ||| || ||   |||   | |  |  |  ||| | |            ||  ||  |  | || |  |  | ||||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||| || ||||| ||||| ||| | ||||| ||    ||| |||
---------------------gtaagagcctcttcaacttttt---ttaagttcccctttcactgaaatttgccttgtataatcctgtcttttaaatatcagCCTGAATGGATGGCACCTGAAGTGCTTCGAGATGAACCATCCAATGAGAAATCTGATGTCTATAGCTTCGGTGTTATCCTATGGGAACTAATGACACTGC

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtatacttt---caaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttga-actcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
||||||  | |||     ||||    |    |      |      |   |   | ||| | |||   | || ||  ||| |    |||   |||  | || | |||| ||||||||||| |||||||| || || |||||||| || ||||| ||||||||||| |||||||| || ||||||||||||||||| || |||||||
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctattt-ccaatggaagctaaataattactgactttgatata-tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtatactttcaaaacgt-gtatcttccttttgaatcgtttgattcagatgtcat---ttttattattgcaaat-taagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
|||||| |   |     |  | | | |    | |    || ||  ||| || ||  ||   |  | || |  ||||| |||  |  ||   |||   |  | | |||||||||||||||| |||||||||||||| |||||| |||| ||||| ||||||||  | || ||||||||| | ||||||||||| || ||||||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttca-tcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC

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|254324293|gb|GR840610.1|GR840610
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
EST: gi|193725665|gb|FK661975.1|FK661975
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCCCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
EST: gi|207837906|gb|GD809442.1|GD809442
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
EST: gi|193648544|gb|FK598355.1|FK598355
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCCCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
EST: gi|193597983|gb|FK552847.1|FK552847
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCT
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCT
EST: gi|254324292|gb|GR840609.1|GR840609
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACTgtaagtatac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
                                    ctcctttttctctact  CT-rich tract
         atttttattattgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT