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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC

Basic information

species Zea mays
transcript GRMZM2G040600_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
                   |    |||    | |  || | | | | |  || | |  |  |  | | || |     |       |||||| | |  ||||| |||||||| |||||||||||||||||||| || ||||||||||| || ||||| |||||||| |||||  | ||| |||| ||||| |||||||| |
---------------gtaatatcgtgaggcctctgatgtttcctaattactgtt-acctagtcttaagatgttaacatatctctctcctttttct--cagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 4
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcct-ttgttttgc-------agGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
          ||     |||||   || |  || |    | ||    |      ||     |  | ||  || ||  |  | |  |  | |||||||||       |||| ||||| |||||||||||||| || |  || || || ||||||||||| || ||||||||||||||||| |||||  ||||||||||||||||  |||
---------gtatgg-ttttggctggaatccttccacagtgcagtgtttcctgagaaacattgatcaatgattggcttattctccttttcttgttttgctacttgcagGAATTCAAAGGTTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 3
gagttgaatttac--aaactttgggatgactta---tttcttga---tccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgt-tttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
|  | |  ||| |   |||  |   ||     |   |||| |||   | | |||       ||||     | |    |||  ||    | |  |  ||  |  || ||||| ||||| || ||||||||||| || |  || || || ||||||||||| || ||||||||||||||||| |||||  ||||||||||||||||  |||
gtatggtttttgctggaacccttccatagtgcagagtttcctgaagttacctgagaaacattgatcaatgattggcttatccgtcctttcttatatttgctacttacagGAATTCAAAGGCTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
----gagttgaatttacaaactttgggatgacttatttcttgatccat-gactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
    |   || |  |  |||| ||   || |||| ||||   |||  | ||       ||||   ||  || |   |        ||   |  |     |   |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  ||||||  ||| |||
gtatgctctgtagatcaaaaccttcaaat-acttgtttcaatatcttttgaggagcattgata--attattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 3
----gagttgaatttacaaactttgggatgact-tatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtga-tatgttcctttgtt-ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
    |  |   |  |  |||  ||   ||  |  | |   ||| |||   | | | | ||  |   || ||||  ||   |     ||| |  ||||| |  || ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| |||||||||||||| ||||| |||||  ||||||||||||| ||  |||
gtatgtttgttagctggaaatcttattatatcaatgtcagttgttcct--attttaggtggagctttaattaatgatctattaacctatataactttgctactgaagGAGTTTAAAGGATATGTTTTCAAAATCACTGGTGGGTGTGACAAACAAGGATTCCCAATGAAGCAGGGAGTGTTGACCCCTGGTCGTGTTCGACTCTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgc------agGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
    |    |    | ||          |||| |||   ||  |  || ||  |  ||    | | | | || | | |  ||   ||  |   |||||      ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
---gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaat-gatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaa-atataggtgtgat-atgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
  ||    | |  |     |    | |  | | || |    |   | |  ||||||  | ||| | |  || ||       | |||   || |      ||||| || ||||| ||||||||||| || |  || || |||||||| ||||| || ||||||||||| |||||  ||||| ||||||||||| | ||| |||
--gtatgctctttagctgctaaccttaaatgtctcct----ctgaatttctgctgaatttataatgattatctattcaccttcatgactctgttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACCGGAGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTGACTCCTGGTCGTGTTAGACTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgt-tttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
  ||  |||||     ||   || | | |  ||| ||     ||| ||  ||        ||||||||  | |  |||| | ||||      | ||||||||| |||||||| || || |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||| | ||| | || ||||| || ||| |||
--gtgaaattttt--tctcctggttcagtgttttttt--ctgatgtcttgtgagttcagtatacttaa-cagaattgtg-tgtgttttgagctatttgcagGAATTCAAGGGATACGTATTCAAGATCATGGGAGGATGTGACAAGCAAGGTTTCCCAATGAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gagttgaatttacaaactttgggatgacttatttcttgatccatgactctt-gctgatg-tcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
     || |  | ||| |  ||||||   | |    | |   |||       ||   || |||| | ||  ||   |     | |||  ||||  |     |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||||||| |||
gtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtt-----tatgaattgttgtt----attgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
gagttgaatttacaaactttgggatgacttatttcttgatcca-tgactcttgctgatgtcatacttaaatata-ggtg-tgatatgttcct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
       |  |||| | |     ||   |  |   |||||| | ||| | |      |  |||    ||  | | | || || | ||||  |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||||||| |||
-------aggtacagattcc---atttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
     | |||||| |   |||  |||    ||  |   || |     ||   ||    | ||| | | || ||  | || | ||||  ||||| |  ||||| || || || ||||| ||||| |||||||| || ||||||||||||||||||||||||||||| ||||| || ||| ||||||||||| | ||  |||
-gtaagcatttacca---ttgttatg--caatgccaaaattctactatcagactagatttata-taacatttatttttgtt-tgtttgtttgtgtgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
          ||  |  ||||  |  | |  | |   |||   |  | |||  | | |    | |||   ||   | | |   ||      ||||  |||||||||||||||||||| ||||| || ||||| || |||||||||||||| || ||||||||||| |||||  ||||  | || || || |  |||||||
---------gtatga-ttttgttactattcttcttaggataacttgccctttgttaggaatgatttattgatgtatcttaagcgt------gtttgacagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
  ||     ||     || |    |  |  | || || |||    | | ||  |||| |  || | | | | |      | |||| | | || ||  |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||| || |||||||| |||||  ||||| |||| |||||| | ||| |||
--gtatgccttttctgctct----tctcccacttatttatctcatattgtt--tgatctactaatcatacaaa------acatgt-catctgcttcacagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S253_38V6.1 (Physcomitrella patens), 3'ss of exon 2
--gagttgaatttacaaactttgggatgacttatttcttgatccatg-actcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagG-AGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGG-TCGTGTTCGCCTTCTGC
  ||   | | |   | | |  || |||    |  | |  || |    |   | |  | | || ||      |   | | || |  || | | ||||  |  |  | ||| | |   |    ||         ||   |  ||||| |||  ||       ||||    | | | | || ||||  | || ||   | || |  |
cagataggcagtgcgagattcaggaatgcgccacctttatatacgcctagcatgggagctctcttatcggtcttcggctttgtttggtgcttgtgttcagTCGCCAATTCTACGACAAGAGATTGGCCCAGGAGGTCAGCGGTGACCAGCTGGGA-----GATGAGTTCAAGGGGTATGTCTTCAAGATCATGGGAGGCTGCGAC

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcag-
                                                                            || |  || |     | || |    ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || |||||    || ||||| |  || |||          
----------------------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 2
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
                                           ||| |    | |   |    |||   | |   |||  || |    ||||   ||||||| ||||| || |||||||||||||||||||| |||||||||||| | || ||||| |||||||| || ||  | |   |    ||||| ||||| ||| 
------------------------------------------gtgaattcgtcggcatttgagctttgctgtt--tgttctaag---atttgcagtgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGT

upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ26393 (Selaginella moellendorffii), 3'ss of exon 2
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
                                           ||| |    | |   |    |||   | |   |||  || |    ||||   ||||||| ||||| || |||||||||||||||||||| |||||||||||| | || ||||| |||||||| || ||| | |   |    ||||| ||||| ||| 
------------------------------------------gtgaattcgtcggcatttgagctttgctgtt--tgttctaag---atttgcagtgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC
     tgctgat  putative branch site (score: 3)
                                     tgttcctttgtttt  putative PPT
             tcatacttaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - atccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttcct