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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC

Basic information

species Zea mays
transcript GRMZM2G123537_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g57390.1 (Oryza sativa), 3'ss of exon 9
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                   |   ||      ||  | || || ||| | ||   || || | || ||    |  ||  | |||    |||||    || |    ||| | |||  | | | |||||||||||||||||||||||||| || ||||| || |||||||||||| ||||||| |||||||||||||||||||||||||| ||||| |||||||| || |
------------------ttggaataagatattgcttttctaaaat-gata--ccgttgctgtggtgg-atatcat--ggctca---cattcctctaaaatgattaaagcaaatgtttcttctccagGCAATGATGAAAGACCAGTTTGCTAACTACGTGGTGCAGAAGGTTTTGGAGACTTGTGATGACCAGAACCGTGAATTGATCCTTTCACGTATCAAAGTAC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G32230.1 (Glycine max), 3'ss of exon 11
gtttgttttcaacattcagtctcatcttgcctttttcttt-tagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                       ||      | ||| ||| |||||     |||   | | | |  ||       ||   |   || || |  |||  |   |  |    |||  | |  |  | ||||| |||||||| ||||  || | ||| ||||||||||| |||||||| ||||| |||||||| |  |  | |||  |||| ||||| || |||||||| |
-----------------------attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggc-tcttagtgaa--tgatggcataacatcaatt--tgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                                      | |  ||||  ||  ||  |  | |  | |||||   |    |||||   |    ||   ||||     || ||   | ||     ||||| |||||||| ||||  || |  |||||||| |||||||||||||| || ||||||||||| || |  | || | | |||||||| || ||||| || |
-------------------------------------gtctgcaatc--taactccctcatgtctttctgcaatgt----ctcgaaaaa----agtcccactaaagttggaacaatttg-----cagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv13s0019g04640.t01 (Vitis vinifera), 3'ss of exon 9
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaa--tgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
     || | |  |    || | | ||||  | ||| | |    |||          || ||  ||  || |  | || |  |          |||||||||  | |  || ||| ||        |||   |||||||||||||  || | ||||||||||||||| |||||| | ||||| |||||||| ||||  || || |||||||| || || ||||||||||
-ccctttatgagtaagaggttttaacttgtttatttatct----atc---------ctgttcatctagtgaaaaagtgtagactg--------agcaacactgatgaattgcaaaattg-------cagATCATGATGAAAGACCCATTTGGAAACTATGTTGTGCAAAAGGTTATTGAGACTTGTGATGATCAGACTCGAGAGTTGATTCTCTCTCGCATCAAGGTCC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------gtttgttttca--acattcagtctcatcttgcctttttcttttagaatcggtagttcgat---ggtctgctgc---tgcaggattggactcgatgc-attctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                                           |||  |  |||      |   |||  | || | || |     ||   |   |   ||| |   |||||  |      | ||||  ||      ||  ||  |     ||  | | ||   |  || |||  | |||||||||||||| |||||||| ||||| || ||||| ||||||||  |||| || ||||||||     | || ||  || | |||  ||| ||    || |
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgc-tgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                            |  || | | | | ||    |  | |   || | || ||  |||   | | |  ||   | || |     |      | ||||    | ||||  | ||||||||||||||||||||||| |||||||| || || ||||||||  |||| || ||||||||     | || ||  || | ||    |||||   ||| |
---------------------------ggatttgtacctgtggaggaagctgatttgtgttatggtgaatgcctcaattgtttccg-gtatgcgtatgagtagcctgatgttcggtgatgtgatgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S96_110V6.1 (Physcomitrella patens), 3'ss of exon 9
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                        || ||   |  |   |  |   |||| |   | ||    |  | || ||   | | || |||  |          || | | ||||    | |||   | |||||||||||||||||||||||||||||||| || || ||||||||  |||| || || |||||   | | || ||| || | ||    |||||   ||| |
----------------------tgtcgtgtggtggtgcatatggtgcggtggagggttga---gtgggtgtagaggtaggct-gatttacagggagctgacgt-tgatgttgggtgatgctgtgcagGCAATGATGAAAGACCAGTTCGCAAACTACGTGGTCCAGAAGGTGTTGGAAACGTGCGATGAGTCGCAGCGCGAACTGTTGCTGGGTCGTATTCGGGTGC

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|47961753|gb|CN844462.1|CN844462
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|211232325|gb|FK959922.1|FK959922
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|89760633|gb|DY688965.1|DY688965
EST:     TAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|60394394|gb|DN227264.1|DN227264
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|60355644|gb|DN222617.1|DN222617
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|113702621|gb|EE680125.1|EE680125
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|60355743|gb|DN222716.1|DN222716
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|60398356|gb|DN231172.1|DN231172
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|60399207|gb|DN232021.1|DN232021
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
EST: gi|166551495|gb|EG205460.1|EG205460
EST:     TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGC
genomic: TTCTAATCAATGAAATGCTTGGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGC
EST: gi|60357180|gb|DN224153.1|DN224153
EST:     GGCACAACTGATGAGAACGAGCCGTTACAG                         GCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG
genomic: GGCACAACTGATGAGAACGAGCCGTTACAGgtttgttttc ... tgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC
                                             tgtcctcc  CT-rich tract
                                taatgtaaacttat  TA-rich tract