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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
|||||||||||||   |||| | ||||    ||||||  |||||| |||  ||    |   ||||||||||||| || |||| | |||| |||     ||||||| |||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| 
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcat----atgcatatgtttattctgatgtggcttgtttttttt----catggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgt-ttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
                     ||||   ||  |   || |||    |  | |||    | | || || || ||||  | ||   |||  || |      |    | ||||||||||| ||||| ||||| ||||||||||| ||||||||  | || ||||||||||| || ||||| ||  | 
--------------------gtttcg-aaaacatgatcttgaagtct--tcatcttgtattttacgtgttgttcttgtctgaaatatagtgatga----aaattttcagACAATGGCTTGGATTCTTGATGAATACTCAAAATTCCATGGACATTCTCCTGCTGTTGTCACTGGAAAACCCATT

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatgga---tgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
                      ||| | ||     ||||  |   ||    |    |   | | | ||| |   |  ||     |  || ||  |||  ||||   ||||||||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||  | 
---------------------gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
gttattttcctttatgtatcatttcatgaaggactttcatgagaa-ttagttatcaataaata--tatgtttattctaa-tatggcctat---tttgtttgctttatggatg--cagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
                 |  |    |  ||  |   | |||  |  || | | | |||    |   || |||   |||| | |||| | |   | || ||  | | | | ||  ||||| |||||||||||||| || || ||||| || || ||||| |||||||||||||| ||||| ||||||||| | 
-----------------agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaaccatatttgaactaactgtggcttttgtttctggttcttgtgttgttgaacagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ36429 (Selaginella moellendorffii), 3'ss of exon 3
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
          ||| | | || |||| |   ||  |||| |      || || ||  |       | | | | | ||  |||  | |  |||||  | | |     ||||| ||||| ||||| |||||||||||||| |||||||| || || || || ||  | || || ||||||||  | 
---------gtttttctctcttttcttt--ggtttttcct-----ctacttgtccttt----cttttctttgcgaagttggattttcatgttt-ttgtttcttcacagACCATGGCTTGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTT

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 3
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
||| || ||  || | | |  |||         || |  |     ||  || ||  |    |  ||   ||| | || |      |||||||| ||| |      ||||| ||||||||||| |||||||||||||| |||||||| || || || || ||  | || || ||||||||  | 
gtttttctctcttttctttggtttttc------ctctacttgtcctttcttttctttgggaagttg--gattttcatgt------ttttgttt-cttca------cagACCATGGCATGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTT

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|148981458|gb|EE027657.2|EE027657
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|148934217|gb|EC878238.2|EC878238
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|60354014|gb|DN220987.1|DN220987
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|87152935|gb|DY397724.1|DY397724
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|22935999|gb|BU572274.1|BU572274
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|148940231|gb|EC885000.2|EC885000
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|20299950|gb|BQ162893.1|BQ162893
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|211300259|gb|FL012334.1|FL012334
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|78092010|gb|DV520384.1|DV520384
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|13125987|gb|BG316662.1|BG316662
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|78089717|gb|DV518091.1|DV518091
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|91867926|gb|EB399854.1|EB399854
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|149101283|gb|EE187396.2|EE187396
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|22491555|gb|BU051478.1|BU051478
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|87156586|gb|DY401375.1|DY401375
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|149110227|gb|EE190296.2|EE190296
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAATTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|19351039|gb|BM895571.1|BM895571
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGNTACTCACCN
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACC-
EST: gi|26559718|gb|CA831953.1|CA831953
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
EST: gi|60357158|gb|DN224131.1|DN224131
EST:     TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAG                         ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT
genomic: TTGGCATCCATACTGACGTTCCAGCTCCAGATATGGGCACCAACTCACAGgttattttcc ... atggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
                 ttctaat  putative branch site (score: 2)
     aatatatgtttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT