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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

Basic information

species Zea mays
transcript GRMZM2G109987_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
|||||| |||  |||||     ||   | || ||| ||||||  |   |||||  |||| | |  || ||| || |||   | ||  |  |||||||  || |||||| | ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
gtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgcta-tcttaactgcctttta--tcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatc-ataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
         | | ||||  | ||  ||   |||     ||||| |  | ||     |  |    ||  | |||   |  | |  || | || ||||   |||||||||  | ||||||||||| || || ||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
--------gtaaatctgagcttcatgaagtgga-----gttgctt--cttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttg---cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 3
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatca-taataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
         | ||||||  | ||  ||   | |     ||||| |  | ||     |  |    |   | |||   |  | |  ||   || ||||   |||||||||  | ||||||||||| || || ||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
--------gtaattctgaacttcatgaagtgaa-----gttgctt--cttttgtggtgaagttttgctcaaattggtttttctgttgtgatccttg---cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG

upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
                       |  ||    ||| ||| |    ||     |  |||| |  || |  |  |      |    |    || | || | ||| | ||  | || ||||||||||| ||  |||||||||| || |||||||| || || ||| |||||||||| ||||||||||||||||||
----------------------gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgctt-ggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG

upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g04320.t01 (Vitis vinifera), 3'ss of exon 3
gtaa-gtgaatcat------tctggccatctggagaaggattcttgttgcgtaaccttgccat----ttcaagactatc-ctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
|||| || || |||      | | | | |||| ||||     ||| |   |||   |||| ||    ||    | |    ||  | ||      | |||  |   |  | ||| |||||  | || || |||||| || |    |||||||| ||||||||||  || || ||| |||||||||||||||| ||||||||||||
gtaatgttaaccatcagcaatattgacctctgtagaactccacttttgatgtaggtttgctatcattttttcaattgcagctgctgatgcacttaatcctttatgttctacagGCTCCTCTCAATAGCTGAGGAGGCCATGGGGGAGTTCCTTTCAAAGGCTAAGGGAACTGCTGTTGATTGGGTCCAGATTCCTGGGATGAAG

upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatc--ataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
    || |    |  |    || |  |  ||   ||| | |   |   ||   ||| |     | ||  ||||    |  ||  ||| |  | ||| || |||||||||  | |||||||||||||| ||  |||||||||||||||||||||| || || ||| | |||||||||||||||||||||||||||
----gtaatgtctaatacaaatgtccatcagttctctggctattt---ctctacatgt-ggatccattgtaattcagtggtatgatttctttgctttttgcagACTCCTCTCCATTGCAGAGGAGACTTTGGCAGAGTTCCTCTCAAAGGCTACAGGAACTGCTGTCGATTGGGTCCAGATGCCTGGGATGAAG

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|30087093|gb|CB885301.1|CB885301
EST:     AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGG                         ACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGGgtaagtgaat ... cttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC
EST: gi|28873580|gb|CB329550.1|CB329550
EST:     AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGG                         ACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGGgtaagtgaat ... cttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC
EST: gi|21809883|gb|BQ668201.1|BQ668201
EST:     AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGG                         ACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGGgtaagtgaat ... cttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
                    tcctaat  putative branch site (score: 2)
                                           ttcttgtttc  putative PPT
                       taatcataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG