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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA

Basic information

species Zea mays
transcript GRMZM2G026470_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gtaggccgcccgagacggaccaataatccccactccccatatct-----agagtcttttacttaccaagcaaag-----cgctggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
                                    |        | ||   |  |||||            |  | |     | |  |||  |||   |  |||        || |  |    |||||||||||||| ||||||||||| || ||||||||||| || || ||||||||||| | |||  |  |||||||||| || ||||| ||||| ||||| |
gtaagtaaatcaatccattcatctctgctaagtcaaactttattagggagaaaaaaataacttttgtcatttaagtatcggcaacaagcttacactgcacctgcatttttttccgtttcatgaacagGGAGAGAAGGATGACAAGATCATAGCTGTCTGCGCCGATGATCCTGAGTACCGCCATTTCAATAATCTCAGCGAGCTTTCTCCTCATCGCCTTCAGGAAA

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtaggccgcccgagacggaccaataatccccactccccata---tctaga---gtcttttac---ttaccaagcaaagcgctg---gaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
         |    ||| ||    |      |  |     |     | |   | | ||   || || | |   ||| |||    ||  |||   | | ||||||| |||||||||||||||||||||||||| || |||||||||||||||||| | || | ||| ||||||| ||||||  | || |||||  |   |||||
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagcaacgtgagatctgttcggaatgcagGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGAGCTTCCACCGCACCGATTGGCGGAGA

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gtaggccgcccgagacggaccaataatccccactccccata---tctaga---gtcttttac---ttaccaagcaaagcgctg---gaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
         |    ||| ||    |      |  |     |     | |   | | ||   || || | |   ||| |||    ||  |||   | | ||||||| |||||||||||||||||||||||||| || |||||||||||||||||| | || | ||| ||||||| |||                          
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------gtaggccgcccgagacggaccaataatccccactccccatatctaga-gtcttttacttaccaagcaaa----gcgct-----ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
                                     |  |   |    |  || ||      |  | |   | || |||    ||   ||  |   || | ||        |     |||  || ||||||||||||| |||||||||||||| ||||| || ||||| || |||||  | |||| ||| |||||||  ||| |  | || || || ||    || |
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctgga--attgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
                     || ||||  |  | | | | |||  |    |  |  |   |    ||  | ||||    | ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||| |   |||||| | |||||||  || ||| | || ||| | ||    ||||
-------------------gtaacaatcatc-ttgctcttgtctgaa----tgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaat--tgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
                     || ||||  |  | | | | |||  |    |  |  |   |    ||  | |||| |  | ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||| |   |||||| | |||||||  || ||| | || ||| | ||    ||||
-------------------gtaacaatcatc-ttgctcttgtctgaa----tgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA

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|20300588|gb|BQ163531.1|BQ163531
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|78121802|gb|DV540186.1|DV540186
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     ATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: ATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|20300295|gb|BQ163238.1|BQ163238
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTTTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGCCCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     ATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: ATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccactccccatatctagagtcttttacttaccaagcaaagcgctggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
                         tacttac  putative branch site (score: 1)
                      ttttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA