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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

Basic information

species Glycine max
transcript GLYMA13G21480.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||||| |||  |    | || || | |||  |   | ||   ||||||   ||| |  |   | ||  |  ||      ||    |    | |  ||||||||||||||||| ||||| ||| |  | ||||||||||| ||||||||||| ||||| |||||||||||||| ||| ||||||||||    |||||||
gtaagttcatattacc----gttacttttatttgttgattttt---tttcagc--taaatcgtgctagtaagtgctt------tcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 13
gtaagt-tcacattga--ctgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttataactatatt-tttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||  ||  |  |  || ||||  ||     ||   |   ||| |   |   || ||   || ||   |   || | |  || || | |  ||      |||||| || |||||||| || || || ||  | ||||| ||||| |||||||| || ||||| ||||| |||||||||||| ||||||| |||   ||| |||
gtaagtaccatttccattcttcagaagttcacccttca-atccctttttcattgaaaatattattcatctttggcttatcttgttctttttccatttaaatattagCCCGAATGGATGGCACCTGAAGTGCTCCGAGATGAACCATCCAATGAGAAATCTGATGTCTACAGTTTTGGTGTAATCCTATGGGAACTTATGACAATGC

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttt-tataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||| | ||||           ||| |||| ||   | || | |||   | | || | | | |  |||  | ||  ||| |   || |    ||   ||||||||||||||||| ||||| |||||  | || ||||| || ||||||||||| |||||||||||||| |||||||||||||||||||||   |||||||
gtaagtt-atattg-----------ttccgtttagtgtattttgt-tttgttacgcaattctatgtggctaagtgtt--attctgtgccatgctatc---tagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcag--aagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
|||||||||  |||  || |  ||   |     || ||  | ||  ||||    | ||    |||  ||    |  |  |   || ||   |||  |   | |||| ||||||||||| ||||| || ||  | |||||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||
gtaagttcagtttgtttgaaactaaaac-acgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttata--actatatttttaatttttctccttttcctccc-ttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
|||||||    |   ||  | |         | |      ||| | |||  |   || |  | ||      | |  | |||  |||    ||||| |  | | |||||||||||||||| ||||| |||||| | |||||| |||| ||||| ||||| ||  | || ||||||||| ||||||| ||||| |||||||||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttcatcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC

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|9820117|gb|BE555627.1|BE555627
EST:     CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
EST: gi|21888649|gb|BQ741862.1|BQ741862
EST:     CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGA-T                         NCTTTATTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAA
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTG-AGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAA
EST: gi|51335181|gb|CO979047.1|CO979047
EST:     CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
EST: gi|19271170|gb|BM887426.1|BM887426
EST:     CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
EST: gi|51344716|gb|CO985449.1|CO985449
EST:     CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
EST: gi|254346794|gb|GR856516.1|GR856516
EST:     CACGTCTGAA-GACAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CGTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG
genomic: CACGTCTGAAGGCCAATACGTTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagttcac ... cctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
                    ctatatttttaatttt  CT-rich tract
        taagttttataactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT