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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccacagtttttatttattatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA

Basic information

species Zea mays
transcript GRMZM2G133698_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
gtgagctccacagttttt----atttattatgatataccgatt----tgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
|||||||||| |||| ||    |  | |||| | ||   | |     || |  | | |||| ||||||| || |||  || ||     |||||| |||||||||||| || |||||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||  ||||| |
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttattt----ctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA

upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctccacagtttttatttattatgatataccgatttgctg---ttgacccttaaccaggcgctaattgttttttctc-ccctacatt---tcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
|| ||   |    ||   |    |||    | ||    || |       || |   |      |  |   |||  |||||     |   ||     || |||| ||||| ||||| ||||| || || || |||||||| ||||| || ||| | ||||||||| | |||||||||||||| || ||   ||||||||
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA

upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctccacagtttttatttattatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
|||||    |  |  || |||  || ||   ||  |||| |   | |     |     |   || |||  |  ||          | | ||||||| || || ||||| || ||||| || || || ||||| |||||||| || || ||||||||| | |||||||||||||| || || | ||||||||
gtgagaattaatgaattgatt--ttctggagtaatgattaggattcgttttatttttggtttctgattactcgtttgt-------tattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA

upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------gtgagctccacagtttttatttattatgatatacc-gatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
                               |  | ||   |  |||| || |||   || ||   || || ||| | |   |     | |  ||||    |||   |  |||   |||||||||||||| ||||| ||||| || ||||| |||||||| || || ||||| || |||||||||||  | |||||||||||||| || || ||||||||||
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctt--tttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA

upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 1
gtgagct--ccacagtttttat-ttattatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
||||| |  | || | |   || | | | |||| |  |  |    || ||          |     |  | | || |  | || | |||||||||| || || ||||||||||| || ||||| || ||||| || || ||||| || |||||||||||| |||||||||||||||| || || ||||||||||
gtgagtttgcaactgataacatgtcaatttgatttctctttgaagtgatgtattggtgtgatttattggtagcttatgtttccttccatttcagACGGGTGTTAATAAGCTTGCTGATCTAGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTA

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|211501121|gb|FL128998.1|FL128998
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
EST: gi|211505822|gb|FL129027.1|FL129027
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
EST: gi|211312615|gb|FL128951.1|FL128951
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
EST: gi|18659978|gb|BM500622.1|BM500622
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
EST: gi|211314638|gb|FL128959.1|FL128959
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG
EST: gi|211505820|gb|FL129025.1|FL129025
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTT-CACTCGGACCAA-G
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctcca ... tacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
                        cgctaat  putative branch site (score: 3)
                              ttgttttttctcccct  CT-rich tract
                           taattgttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccacagtttttatttattatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG