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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccttctcttcccatcctaccgtgcgagacccagcacacgaaccctaacttaagctatttggctatttgcatccggatctgatctaattaccagtgtgtgcatgcctactaacttggattttttctggggaaaaatattcttgggacacccctgtcctttactgggctctcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAGGCGGAGAGGAAAGCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCG

Basic information

species Zea mays
transcript GRMZM2G089630_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 1
gtacgcccttctcttcccatcctaccgtgcgagacccagcacacgaaccctaacttaagctatttggctatttgcatccggatctgatctaattaccagtgtgtgcatgcctactaacttggattttttctggggaaaaatattcttgggacac-ccctgtcctttactgg-gctctcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAGGCGGAGAGGAAAGCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCG---
                                                                                    || | || ||    ||    | | || |  | |  ||||  | || |    |   | | |  | |  | |  | |||  |  ||| |   | ||   | |   | |  ||| || ||||||||||  |||| |||||||| |||| || ||| || ||||| |||||||  || || ||||| |||||||||||||| || |   
------------------------------------------------------------------------------------tggtttattt--tggtactagta-gcttgttga--tggacctcttatttatatctaaactaattgaccgcatcttgtattgaactagtagtttctgatgcttcagATCGGATTGTACTCTACATGATAAGAAAGTATGGCACCAGCAAACAAAGCAGAGAGAAAAGCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGA

upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 1
gtacgcccttctcttcccatcctaccgtgcgagacccagcacacgaaccctaacttaagctatttggctatttgcatccggatctgatctaattaccagtgtgtgcatgcctactaacttggattttttctggggaaaaatattcttgggacacccctgtcctttactgggctctcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAGGCGGAGAGGAAAGCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCG
                                                                | |  | | | ||   ||| | |  |  ||     | |||||||   ||    |||  ||| ||            || |      |     ||    |  | || | |   ||  |    ||| |||| | || |||||||| ||||| |  ||||| || ||||||||||| ||||| ||||||||| |||| |||||                    
--------------------------------------------------------------actagtgactcgtatt--gatttcacttgttttttc-tatgtgcatttatatatgcttatattattaaactcatgtcttaattaaaatatgtttctaatgtagATTGTGATACTCCAAAATCCAAATTGGATTAGATTCTACATGACAAGAGAACATGGCACCTGGAAGCAAGGCAGAGAGAAAAGCAGCATTAGATGCTGGA-------------------
















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|211182574|gb|FL404769.1|FL404769
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGWAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|24462536|gb|BM660067.1|BM660067
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|148965218|gb|EE016025.2|EE016025
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211127243|gb|FL371391.1|FL371391
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211219466|gb|FL394123.1|FL394123
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211212172|gb|FL397455.1|FL397455
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211148954|gb|FL408689.1|FL408689
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211059840|gb|FL382528.1|FL382528
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211163062|gb|FL403922.1|FL403922
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211125396|gb|FL373706.1|FL373706
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211395001|gb|FL377443.1|FL377443
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211269202|gb|FL409758.1|FL409758
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211421251|gb|FL404519.1|FL404519
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211439743|gb|FL418515.1|FL418515
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211231674|gb|FL380035.1|FL380035
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211176599|gb|FL421415.1|FL421415
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|148931222|gb|EC873991.2|EC873991
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211030447|gb|FL427837.1|FL427837
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGACTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211403472|gb|FL414959.1|FL414959
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
EST: gi|211421497|gb|FL416796.1|FL416796
EST:     AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACTCACCAG                         AAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG
genomic: AGGTGCCCAATTCCTCGTCGGGTCCTCCGCCGGCGACGAGCACCCACCAGgtacgccctt ... tcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggggaaaaatattcttgggacacccctgtcctttactgggctctcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAGGCGGAGAGGAAAGCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCG
                                          ctctcccctac  CT-rich tract
      aaaaatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcccttctcttcccatcctaccgtgcgagacccagcacacgaaccctaacttaagctatttggctatttgcatccggatctgatctaattaccagtgtgtgcatgcctactaacttggattttttctggggaaaaatattcttgggacacccctgtcctttactgggctctcccctacagAAAACTGGAGTGGACTCTACATGTCAAGACAGTATGGCGCCAGGAAGCAAGGCGGAGAGGAAAGCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA