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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattgtccacaataattcctccagcattgggcctattctgtttggcatggcatgactaactatcaaatttgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTGTTGGAATATG

Basic information

species Zea mays
transcript GRMZM2G150058_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
gtatgaattgtccacaataattcctccagcattgggcctattctgtttggcatggca--tgactaactatca--aatttgtcttg-cagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTGTTGGAATATG--
|||  ||| |   |   | | |          ||       |   || | ||||  |  ||| ||  |||     || |||  |  ||||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||||| || ||||| ||||  |||||| ||||     
gtaacaat-gcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAG--CTTGTTTGAATGAATT

upper sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S73_232V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------gtatgaattgtccacaataatt----cctccagcattgg--gcctattctgtttggcatgg---catgactaac-tatcaaatt--------tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTG-TTGGAATATG
                               || | | |    | | |     |  ||||||  |  ||   ||    ||  ||||     ||  || || | || | |         | | ||||||| |||||||| |||||||| || || ||||| || || ||| | ||||| ||||||||||| || || |||||||||||||||  | ||  || ||   | 
gtaatttattactatcacgtcgttggactcaaactattctttgtgaatgggatcggcagcataagcggcgagttgatgttttcatgaatatattcctgacctgtcgagtgccctctggttttttgcagGGTCCGCTATTACTGGACCAATTGGGAAGGAATGCGCAGATTTGTGGCCCAGGATTGCTAGTGCCGCCAACGCCATTGTTTGAAGGTTTACTTCGAGAGT-

upper sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S280_69V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------------gtatga-attgtccacaataattcctccagcattgggcctattctg---tttggcatggca----tgactaactatcaaatttgtc--------ttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGC--TTGTTGGAATATG
                                                                                       ||||  || ||      |  ||     |   ||| ||   || ||   ||||| |||       ||| | |||   |  ||| |         |||||||||| ||||||||||| ||||| || |||||||| || ||| | ||||||||||||||||| || || || |||||||| |||| ||  | |||| ||||  
gtacgcagatatttccctcaaatatctttgacgtcagattcgttttagcaaaagatccagttagcgaatgagaatgattggcagatatatgtcatcgtatgttgttcttatcggaatgttgtgcacgttatgacttttgggatgagcctactgatttactgataggttttttggcaacttttgcagGTTCTGCTATCACTGGTCCTATTGGGAAGGAGTGCGCCGATTTGTGGCCTAGGATTGCTAGTGCTGCCAATGCCATTGTCTGAGGGCAATAGTTGTAATA--

upper sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------gtatgaatt----gtccacaataattcctccagcattgggcctattctgtttggcatggcatgactaactatcaaatttgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTT-GTTGGAATATG
                                             | |||        |         ||  ||  |   | | |  |    ||   |   ||    |  |          | |    ||||||||| || ||||||||||| ||||| |||||||| || ||  | ||||| |||||||| ||||| || ||||| ||||||||||||  | ||| |    | 
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT-

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|113667987|gb|DW814997.1|DW814997
EST:     GTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: GTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|76015614|gb|DT942784.1|DT942784
EST:     ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|76015615|gb|DT942785.1|DT942785
EST:     ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|166514420|gb|EG083069.1|EG083069
EST:     GTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGAACCTAATCGGCAAGGAGTGTGCTGATCTTTGGCC
genomic: GTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGG-ACCT-ATCGGCAAGGAGTGTGCTGATCTTTGGCC
EST: gi|113843951|gb|DW971861.1|DW971861
EST:     GTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: GTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|149087575|gb|EE176972.2|EE176972
EST:     ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATTTTTGGCCTA
genomic: ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|166450390|gb|EG107710.1|EG107710
EST:     AGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGACAAGGAGTGTGCTGATCTTTGGCC
genomic: AGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGG-CAAGGAGTGTGCTGATCTTTGGCC
EST: gi|166574257|gb|EG154583.1|EG154583
EST:     AGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCTGCAAGGAGTGTGCTGATCTTTGG
genomic: AGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGG
EST: gi|166410585|gb|EG285148.1|EG285148
EST:     TGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: TGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
EST: gi|71431101|gb|DR812151.1|DR812151
EST:     ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAG                         GTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA
genomic: ATTTGCAGATAATGCTGGAGTGATTGTGAATCCCAAGGGTGAGATGAAAGgtatgaattg ... tgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgggcctattctgtttggcatggcatgactaactatcaaatttgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTGTTGGAATATG
                             gactaac  putative branch site (score: 1)
                                           tttgtctt  putative PPT
                                taactatcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaattgtccacaataattcctccagcattgggcctattctgtttggcatggcatgactaactatcaaatttgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTGTTGGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT