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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT

Basic information

species Zea mays
transcript GRMZM2G118467_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
gttggtgcatggagactcacccacgcacacagtagactttaattctatg--tttgcagcttctgtatattcattttc----ctctaataagattgtgcttattcttttgatgatggcg-atgtttgttctc---tttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
||  || | ||||  |      |      | |||  |||| ||  |||   |||| |||||| ||| |    ||||      |  |     | |||  | |  | ||| ||||||||  |   ||| | ||   |||||||||| |||||| ||||||| || || ||||||||||||||||| ||||| |||||||||||||| || || || || ||||||||||| || ||||| ||
gtcagttcctgga--ccagtttatat---ctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                                       | |   |    ||  | | | |  |||  |||  |      ||    |||| |  | | || ||| || |       ||||  |  ||||||||| ||||||   ||||| |||||||||||  |  ||||||| || || || || || |||||||| || || || ||||||||||| |||||||||||
--------------------------------------gtgagcatggtgttatatcattttgataaacataatatctgtatc---ttgttcacaattttatgaaga-gatatgacttgtggt--ttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTGCTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataag-attgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                                             |  |  ||  | |     || || ||   | |   ||  | ||  || | |   ||||    |  |  |||  | |    |||||||||| ||||||   ||||| |||||||||||  |  ||||||| || || || || || |||||||| || || || ||||||||||| |||||||||||
--------------------------------------------gtgagcatggtgttatatcattttgataaacttaatatctgtatcttggtcacatttttatgaaaagatatgact-tgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgt-ttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttct-ctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                                          |   || | |||||   |      ||| ||||        ||| ||  || | | |  ||| ||||  | |||   | || |  |||||||||| ||||||   ||||| ||||| ||||| || |||||||| ||||| || || ||||||||||| || || || ||||||||||| || ||||| ||
-----------------------------------------gtgtgatatcttgcaatgttatgtcattaatttgataaatttaacatcctgatcaattgttt-atga-agtgataccttttgtgttttcagCGGATTCATTGGTTGTGGAGTCATTGTTGGAGCTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                        |   ||   ||   ||| ||  | |  |    |       | ||   |||| |||   |   || |  ||  |||  | |  |    | | |||||| | ||||||||||| |  | |||||||| || || |||||||| |||||||||||   ||| || || ||||||||||| ||||| || |||||||| || ||||||||
------------------------gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatct--cagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G58580.1 (Arabidopsis thaliana), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctcta-ataagattgtgcttattcttttgat-gatggcgatgtttgttctc---tttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                                          |||    |||  | || |  | |  |  |||||  ||| || |||     |   ||   || || |   |   | |||||  |    ||||||||||  |||| |  ||||| ||  |||||||| |  ||||||||||  | |||||||||||||||||||| || ||||| |||||||| ||  |||||||
----------------------------------------gtttcaccatttttaactccattgtccttgttttcaactacatcagaaataacaagttaacttaattggaagatttttttgtgtttgggtttcagCGGATACATTAATGGTGGAATCTCTATTGGAATTACTGGATGAAGATGGATTAAGAAAAGACACAGCTCTTCCTTCCCCAGAATGGTCTTCTAATCACAT

upper sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcat--tttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
||       |    ||    |      ||   |   | |  ||| ||| |   ||  | ||  ||| |  |  |||   |   ||    |||      |  | | || |    ||| | || |    | |||| ||||| || || ||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| || || || || || ||||| || ||||| ||
gtaatctttttcctacatgtcggtttgcatctttttcctatattttatttacacatgtgcttcatacttgtagtttgtgccgttattgatgtttaggattctctaataaataagatttgtggt----tccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATAT

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|211427750|gb|FL230782.1|FL230782
EST:     AAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|33092350|gb|CF052344.1|CF052344
EST:     ATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: ATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211013492|gb|FL469772.1|FL469772
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211427747|gb|FL230779.1|FL230779
EST:     TAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211427745|gb|FL230777.1|FL230777
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211427746|gb|FL230778.1|FL230778
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211427749|gb|FL230781.1|FL230781
EST:     TATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: TATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|211241666|gb|FL441721.1|FL441721
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|32824898|gb|CD964620.1|CD964620
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|148934305|gb|EC878331.2|EC878331
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|6194468|gb|AW146572.1|AW146572
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT
EST: gi|32793111|gb|CD945347.1|CD945347
EST:     AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAG                         CGGACTCATTGACAGTGGATTCATTATTGGCACTTTTGGATGAAGAAAGCT
genomic: AAATTGCACAAGAGATTTTACTGGAACTATTGATTACATATTTTACACAGgttggtgcat ... tctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
                                      tgtttgttctctttc  CT-rich tract
                 ttattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA