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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT

Basic information

species Zea mays
transcript GRMZM2G077844_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                                                          |  |||     |  |   |      || |  | |   || || ||| ||    || || | ||| ||||    | |||||||| ||||| || |||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||| || ||||| | |||||
-----------------------------------------------------------------------------------------gtctgctaacactgtttgatgtccttccatgctgaaagattaagatattg----atttattgttttgttt----tctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaacccta----ttcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                                             | | ||| | ||  | |  | | |||     |   | |   |     ||   | ||  |||  |||| | || |  | | || |   |  |||||||||| | ||| |||||||| |||||| |  ||||  |||| |||||||||||||||||||| ||  |  | ||||||||||| || ||||| || ||||
-----------------------------------------------------------------------------gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgt-tgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                                                |  |  |||| |||| |   | | | |       |||  |||   | || ||||  |||| ||   || | | ||     |  |||||||||| || || |||| |||||||||||| ||||| ||||| |||||||||||||||||||| ||  |  | ||||||||||| |||||||| |||||||
------------------------------------------------------------------------------gtattagttttcatggcattcctattttat------acctgatttcatcatgaaaagtatgtttatcatatt-tatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                        | ||  ||||||     |||     | |   ||| |   || |               |||  |||   | || ||||  |||| ||   || | | ||     |  |||||||||| ||||| |||| |||||||||||| ||||| ||||| |||||||||||||||||||| ||  |  | ||||||||||| |||||||| |||||||
--------------------------------------------------------gtattgatatttcttggatgttttcatagccttcctattttat---------------acctgatttcatcatgaaaaatatgtttatcatatt-tatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaaca-aatttcttggcttgtgtttatgagta--agtaaccctattcagta-ataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                                             | | ||| | |||||||  |  | |||  |  |   | |  | || ||   |  ||| | ||| ||| | || |  | | || |   |  |||||||||| | ||| ||||||||||||||| | ||||| ||||| |||||||||||||||||||| ||  |  | ||||||||||| || ||||| || || |
-----------------------------------------------------------------------------gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatata-tgt-tgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                                             || | |    ||||      || | ||| |||     |  ||     ||  ||  | ||| |       | ||   |||  |   || |  |||     |  || ||||||| |  || |||| |||||||||||| ||||||||||| |||||||||||||||||||| ||  |  | ||||||||||| || || || || ||||
-----------------------------------------------------------gtcagact---gtcattcaagtaccatttttttgttccctagtttcatttattta--cttatccg------agaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|211007985|gb|FL246230.1|FL246230
EST:     TTGCTGAGAAGGATAT-----AT-A--TGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|211469270|gb|FL411606.1|FL411606
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|78103934|gb|DV522352.1|DV522352
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|78118618|gb|DV537002.1|DV537002
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|149083221|gb|EE172499.2|EE172499
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|32868858|gb|CF008540.1|CF008540
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
EST: gi|8368846|gb|BE051791.1|BE051791
EST:     TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG                         CCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAGgtgcaaatgc ... tgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
                                      tttcgttt  CT-rich tract
            taataaaaataatgtc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA