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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgataaaccgaatgatcgactctgttgctacaaaatcgtctctgcttgacgcaatggttcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG

Basic information

species Zea mays
transcript GRMZM2G088245_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 2
----------gtgatgata-aaccgaatgatcgactctgttgctacaaaatcgtctctgcttgacgcaatggttcc-cttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG
           |  | ||  || |     |    |||| |||  |   | |  | |||  |||  |||||  ||   | ||||||| ||||||||||||||||||| ||||||||| || |||||||||||||| ||||  |||||||||||||||||||| ||||||
gtaaactaaactattcatgcaaacatggaaaaatctcttttgtgatccact--tttctagttgctgcaatattttttcctctagGTTAGAGTCTGCAGAGAGAAGAACACAGGAAATGTTTATGCGATGAAGAAACTTAGGAAGTCAGAAATGCTTCGTCGTGGTCAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 2
----------------------------gtgatgataaaccgaatgatcgactctgt-----tgctacaaaa-tcgtc------tctgct-tgacgcaatggttcccttct----agGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG
                             | |  | ||||         ||   |       || ||||||| | |||      | |||      |||||  || |||| |    |||||||||||||| ||||||| || || ||  | || ||||| |||||||| ||||| || ||||| ||||||||  |||| |||
gtatagtctgcctttattttcattgaagttaaaaaaaaactatgcttctgatctttcacatatgttacaaaaattgtcagataatttgcaactttgcaattttttccttttttatagGTCAGAGTCTGCCGAGAGAAAACAACTGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtgatgataaaccgaatgatcgactctgttgctacaaaatcgtctctgcttgacgcaatggttcccttct--agGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG
                           ||  |  |  |     | ||    | |  |   ||   || | | |  ||||     |   |||  ||||  |||| ||||||||||| |||||||  || ||  | || ||||| |||||||||||||| || ||||| ||||||||  | || |||
gtttgtggaaaattttctgcactgtctgttttctttgatgctgttataacatttcatttaacttgattg-caccccttgttcttacttttctgttctgtagGTTAGAGTCTGCAGGGAGAAGAAAACCGGCCATGTATATGCCATGAAGAAGCTTAAGAAATCAGAGATGCTTCGAAGGGGCCAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtgatgataaaccgaatgatcgactctgttgctacaaaa---tcgtctctgcttgacgcaatggttcccttct-----agGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG
                       ||  | ||    ||  |   || | |   | |  |    | |    |  ||    || || ||   || |     |||| |||||||| ||||||||||| || || || |||||||| ||||| |||||||| |||||||| |||||||| ||||| |||
atctttttctttcattcagctctatcttgaatttgatcctgtgctgtatccttgcctatcatttgctcattattagtacattgttttatttgtggtgcagGTAAGAGTCTGTAGAGAGAAGACAACGGGTAATGTGTATGCAATGAAAAAGCTTAAGAAGTCAGAGATGCTTCGACGAGGCCAG

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|93015891|gb|EB641411.1|EB641411
EST:     TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAG                         GTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
genomic: TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAGgtgatgataa ... tcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
EST: gi|6695926|gb|AW289034.1|AW289034
EST:     TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAG                         GTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
genomic: TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAGgtgatgataa ... tcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
EST: gi|78180515|gb|DV551008.1|DV551008
EST:     TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAG                         GTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
genomic: TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAGgtgatgataa ... tcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
EST: gi|12045527|gb|BF727666.1|BF727666
EST:     TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAG                         GTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG
genomic: TCGAGGATTTCGAGCTGCTAACAATGATAGGGAAGGGAGCTTTTGGCGAGgtgatgataa ... tcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgactctgttgctacaaaatcgtctctgcttgacgcaatggttcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG
                              gcttgac  putative branch site (score: 4)
                                            ttcccttct  putative PPT
               tacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgataaaccgaatgatcgactctgttgctacaaaatcgtctctgcttgacgcaatggttcccttctagGTCAGAGTCTGCAGAGAGAAGACCACAGGAAACGTGTATGCGATGAAGAAGCTTAAAAAGTCAGAAATGCTTCGTCGAGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC