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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttgtcctactattggcacttaacccataccttttgatattttagttctcttgtgataattagttggtgcttcaataatttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTGGATATGTTTCCTCATACTCCTCATATTGAGTGTGTATGCTTATTGGAGC

Basic information

species Zea mays
transcript GRMZM2G115198_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115198_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g09750.2 (Oryza sativa), 3'ss of exon 8
gtatgcttt-gtcctactattggcacttaacccataccttttgatattttagttctcttgtgataattagttgg--tgcttcaataatttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTGGATATGTTTCCTCATACTCCTCATATTGAGTGTGTATGCTTATTGGAGC
||||| ||| |||||| |||||  |  || ||  ||| |  |  ||||||||||||      |||   | ||    |   |   ||||||| || |||||||| |||||||||| ||||| ||| || ||||||| |||||| ||||| |||||||| || || ||||||||||| || ||| | ||| |  ||||||
gtatgtttttgtcctattattga-agatacccattacttcatattattttagttcttagtgcatagccacttcaattaaatacttaatttgtctacagGAGGAAAAAGATTTGAAAGGATGCTACGAGCTGAAGACTGTAATACCTGTAGATATGTTCCCCCACACTCCTCATATCGAATGTATCTGCGTGCTGGAGC
















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|211307893|gb|FL436435.1|FL436435
EST:     ATCCAGCTACTTGTGCTCGGGATTTGGACTACTTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: ATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|6012611|gb|AW062048.1|AW062048
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|149065678|gb|EE286800.2|EE286800
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|211103900|gb|FL455681.1|FL455681
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|78090076|gb|DV518450.1|DV518450
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTAGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|148945132|gb|EC890330.2|EC890330
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTTTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|50334077|gb|CO529203.1|CO529203
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTTTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|211103899|gb|FL455680.1|FL455680
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|83278825|gb|DV942833.1|DV942833
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|78109730|gb|DV528146.1|DV528146
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|148938312|gb|EC882620.2|EC882620
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTTTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
EST: gi|7118942|gb|AW497529.1|AW497529
EST:     GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTG                         GAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG
genomic: GTAATCCAGCTACTTGTGCTCGGGATTTGGACTACCTATGTCATGGCGTGgtatgctttg ... ttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattttagttctcttgtgataattagttggtgcttcaataatttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTGGATATGTTTCCTCATACTCCTCATATTGAGTGTGTATGCTTATTGGAGC
                                           atttgac  putative branch site (score: 4)
                                    ttcaataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttgtcctactattggcacttaacccataccttttgatattttagttctcttgtgataattagttggtgcttcaataatttgactgcagGAGGAGAAAGATTTGAGAGGATTCTATGAACTGAAGAGTGTAATTCCTGTGGATATGTTTCCTCATACTCCTCATATTGAGTGTGTATGCTTATTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG