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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaataccttgtatttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag

Basic information

species Zea mays
transcript GRMZM2G122135_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgt-atttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag--------------------------------------------------------------------------------------------
||    |||||  | || || || || ||||||||||| |||||||| ||||| || || || |||||||| |||||||| ||||||||||||||| || ||| | ||   |  ||   |    |  |   ||| |     ||   |  ||   |   | |  || |   | || ||  |  | ||                                                                                            
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctg-tgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgt-atttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag------------------------------------------------------------------------------------
||    |||||  | || || || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||||||| || ||| ||||   |  ||   |    |  |  |||| |     ||   |  ||   |   | |  ||     | || ||  |  |  |                                                                                    
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctg-tgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgtatttcctaca-actgtgcataatataatccttctatttcctgcaacctgttctgttttcccag--------
||    || ||| | || || || || ||||| ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||| |||||| || | |   ||     | ||   | |   |  || | ||| ||| || ||| |   |  |  |    | |   |  | | | |||            
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtattatacactatgccta-tatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaataccttgtatttcctacaactgtgcataatataatc-cttctatttcctgcaacctgttctgttttcccag
||   ||||||| | || ||||| || |||||  ||||||| ||||| |||||||| ||||| || |||||||||||||||||| ||||||||||| | | |  |     | |  |  | |||| |  |  |         |  ||  |  ||  |  ||  || |   | || |  ||   |||
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtt-tgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatt-tacttgttcag

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaataccttgtatttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag
||   ||||||| | |||||||| || |||||  | ||||| ||||| || || || ||||| || ||||||||||| |||||| |||||||||   ||| ||||  || |  | | ||| ||       ||  |||  ||  | | |   ||  |||    || |    ||     | | |||
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGg---tttgtctagaatttttacaactt-tagaaaagtcag-tgtctatcttgttagtgtta-attagtcgctattcatt---aatccgcag

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgtattt-----cctacaactgtgcata-atataatccttctatttcctgc--aacctgttctgttttcccag
|| | ||| ||  | |||||||| || |||||||| ||||||||||| ||||| || ||||| || ||||||||||||||  ||||||| ||||||  | ||     | || ||||   |||   ||     | |  ||  |    |  |||| |   |   |||  |  |  |     || || |||  |  
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgtttgtctagtggttgtgacaattaattgctattagtggcttgtaaaggatagtggatatgagtttcaaattctcatcttatttcattttggtttgtctc

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 11
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaatac---cttgtatttcctacaactgtgcataatataatccttctatttcc------tgcaacctgttctgttttcccag
|| |  |||||  | ||||| || || || ||  ||||||||||||| || || || || ||||| |||||||||||||| |||||||| |||||  ||    |   || | | |      | |||  |  || |   |     |  |  ||| | || ||         | |||  |||    | |  | ||
GTTTATTCAATTCGTGATGCAGCTGCTAATAATGTGAAGCGCCTTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctgattacatattactgtgaattggtaccttttaaacaagcattgataaatatcttgctgttcaacatagatacaaagtgtctaatctgacaag

upper sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 5'ss of exon 9
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtc---aataccttgtatttc--ctacaactgtgcataatataatcct---------tctatttcctgcaacctgttctgttttcccag----------------------------------------------------------------------------------------------
|| | ||| ||| |||| ||||| || |||||| | ||||| ||||| |||||||||||| | ||||||||| |||| || || ||||| ||||| | ||  |    | ||     ||    | ||  ||    |  | | || |   ||| | | |         || ||    | || ||| |  |  ||   ||                                                                                               
GTGTACTCTATCCGAGAGGCTGCTGCGAACAACCTTAAGCGTCTTGCCGAAGAGTTCGGTTCCGAGTGGGCATTGCAACACATCATTCCACAGgt-acttgcccgacaagtttgtgatgaggtctaactcggtaatgagtatggaagttatgagcttctctcacagtcgatacattacagcctttgttcgttaaacacacgagctatggttgagagacctgtgtatttgtgataatttttatactactgataggctgagatttttttctgaccatgttgtgaggacttgcag

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|33092634|gb|CF052628.1|CF052628
EST:     ATGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTT
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTT
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAN                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|60340533|gb|DN207506.1|DN207506
EST:     TCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|116828872|gb|EC861659.1|EC861659
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|32914759|gb|CF019571.1|CF019571
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGG-CAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|60352335|gb|DN219308.1|DN219308
EST:     GAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: GAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|211206781|gb|FL154157.1|FL154157
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|33101424|gb|CF061384.1|CF061384
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|60356306|gb|DN223279.1|DN223279
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG
EST: gi|32845037|gb|CD984718.1|CD984718
EST:     TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGAGAAGATCAACAATCCGCACTATTTGT
genomic: TTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGT
EST: gi|6031522|gb|AW076424.1|AW076424
EST:     TGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG                         GTGCTGGACAAGATCACCAATCCGCACTATTTGTACCGCATGACGATTCTG
genomic: TGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatc ... gttttcccagGTGCTGGAGAAGATCAACAATCCGCACTATTTGTACCGCATGACGATTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgttatttatctactatgtcaataccttgtatttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag

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