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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG

Basic information

species Zea mays
transcript GRMZM2G081915_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 1
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                   |     ||| |||    |  ||  ||  |        |  |   |   ||| |         ||   |||  || || |  |||| |      | |  || |    ||||||| || ||||||||||| ||||| || ||||| |||||||| ||||||||||||
------------------gtaggtaaccttgccatttctctcttcccgg------atatatataaccctaccaaaattttgcccatttctttgtaccatccaaaatt-----gtcttttctatccttcagGCACGGTTCTTTTTCCAGCAACTGATTTCAGGAGTCAGCTATTGCCATTCCATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
               | | | ||  |   || || |||| |   |       | ||  |  || |   | | | |  |     || | |      |||  |||  | |  || |   | ||    ||||||| || ||||| || || ||||||||||| ||||||||||| |||||| | |||
---------------gttcttatttaatttgtttacttgttctaca------cctgaacgtta-taagtttgtacttcgaatttgttcc------ctacgcaagtt-tgtaacctgttgttatgattcagGCTCGATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                              |  | |||| |||| | |||   || || |  | | |||||  |   | ||  |    ||||         ||||    | |||||||| ||||| ||||||||||| ||||||||||| ||||| || ||| | |||
--------------------------------------------gttcttatcttttgcattcatt--catttgtgt-aatgctgctgtatatgccttttatgtctgtt---ttttgttttatgctgcagGCGCGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTATTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                    ||  |     | |  | |  |||| |  ||| |  | | ||   | | | | |     || | | |   |||| |      | |||  || ||||| || ||||| ||||||||||| ||||||||||| |||||||| ||| | |||
-----------------------------------gttcttatctattcc-tttcatgcattt-ttgttg-cagtgctgttgcagttaccgcttaccattta---tgtcta---ttatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                        |  | |  ||  ||  || |     | |  |   | || | ||||||  |       | |  |  ||    ||| |     |||  || ||  | ||    ||||||| || ||||| || || ||||||||||| ||||||||||| |||||| | |||
------------------------gttcttatttaatt--tgtttac-ttattctacac-ctgaatgctataagt-ttgtacttattctac---gctagt----ttgt--aacccgttgttatgattcagGCTCGATTCTTCTTTCAGCAACTCATATCTGGGGTCAGCTATTGCCATGCTATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                              |  | |||  |||| | |||   || || |  | | ||||| ||   | ||  |    ||||         ||||    | |||||||| ||||| ||||||||||| |||||||| || |||||||| ||| | |||
--------------------------------------------gttcttatctgttgcattcatt--catttgtgt-aatgctgctgcatatgccttttatgtctgtt-----tttttttatgctgcagGCGCGCTTCTTCTTCCAACAACTTATATCAGGAGTTAGCTACTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                        | ||  | |  | ||||  |||  ||    | |||     | ||  ||| |||         |||| | ||  ||  |  |   |  ||||| |||||||| || |||||||||||||| |||||||||||||| ||| | |||
---------------------------------------gttcttatacaat-ttgtttact--ttttcttgtgctaggtttctatttc-ctgtgt------aactattaac-ccattgatatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgc-tatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctt---tttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                             || || |  | | |  |   ||| | | ||   || | ||| | || |  |||  |   ||  | || |||  ||   |||  || ||||| || ||||| ||||||||||| ||||||||||| |||||||| ||| | |||
---------------------------------------------gttcttttctattcctttcatgcatttttgttgcagttctgttgcagtt-actgctt--accattaatgcctattatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                        | ||  | |  | ||||  |||  |||||   || || |   ||   |  |  |  |||  |        || ||  | |       ||||| |||||||| || |||||||||||||| ||||||||||| || ||| | |||
---------------------------------------gttcttatacaat-ttgtttactt-ttgct---tgtgctagctctctatttcctgtgtaacta------ttaacccattgtcatgccacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG

upper sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 3
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                                        | ||  |||   ||||  || |  | | | ||||    ||||      |||| |  ||      ||  |     |    ||  | | ||||| |||||||| |||||||||||  ||||||| ||||||||||| ||| | |||
---------------------------------------gttcttatgcaa-cttgctcatt--tggttttctgt--tactctcctcgcactcgtttat---ggcttaccttctctagcttgtactgcagGCACGTTTCTTCTTCCAACAACTTGTATCAGGAGTCAGCTACTGTCATGCGATG

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|149112537|gb|EE295397.2|EE295397
EST:     GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAG                         GCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC
genomic: GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAGgtccgtcttt ... ttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC
EST: gi|78080573|gb|DV508985.1|DV508985
EST:     GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAG                         GCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC
genomic: GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAGgtccgtcttt ... ttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC
EST: gi|149005339|gb|EE039890.2|EE039890
EST:     GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAG                         GCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC
genomic: GCGAGCTCTTCGAGCGCATCTGCAACGCCGGCAGATTCAGCGAGGACGAGgtccgtcttt ... ttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG
                  gactaat  putative branch site (score: 2)
                                      cccctttttcatttc  putative PPT
                                          tttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT