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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA

Basic information

species Zea mays
transcript GRMZM2G028037_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 2
gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgctt-gtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
||||||||| | ||  | |  | ||||        | | ||||||||| || ||| ||||||| |||  ||  ||| || | ||  ||  ||| |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||
gtatgttttgaattgct-tcagcatacag-accacaaaatattattcaactgtcttctaatgcatcatcaattaaactagcgttatttcattttcagGCAGAAGTTGATTTTCTTGGAAACCTTCAACATCCACACCTAGTGAAATTGGTTGGTTACTGCATCGAAGATGACCAAAGGTTGCTAGTGTATGAATTTA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 2
------------------------------------gtatgtttttattttttgttggtatactttgttgaaga-gtattattcagctctctgcta-atgcgtcactaagcaaagt---atcattgcttgttt------gcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
                                     | | | |||  ||||| ||  | || ||| || ||   ||||  || |  |   |  || ||||   |   | |||  |   ||  ||| ||| ||       ||||| || ||  ||| ||||||  | ||    |||||||| || || ||| |  |||| ||||||||||||||||| || |||||||| || ||||||||||
gtttgtattttactaatataattgttcattttttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 2
----gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
    |||| |||| |    |  ||  | |  | | ||    | || |           |  |||||  ||  | |     | |||||       |  ||||| |||||  ||||||| ||  | ||    |||||| | || || ||| | || || ||||||||||||||||| || |||||||| ||||||||||| |
gtttgtatattttcaaaagtccttcttttcttctattattaactactgaattctatatttttaatg-atctttcatgtttggatcatg------tgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 3
-------------------------------------gtatgtttt-tattttttgttggtatactttgttgaa-gagtattattcagctctctgcta-atgcgtcactaagcaaagt---atcattgcttgttt------gcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
                                      | |||||  | |||||| ||  | || ||| || || | ||||  ||    |   |  || ||||   |   | |||  |   ||  ||| ||| ||       ||||| || ||  ||| ||||||  | ||    |||||||| || || ||| |  |||| ||||||||||||||||| || |||||||| || ||||||||||
gtttgtattttagtaatataattgttcatcctttgtattctgtttgattttttttttttatgtattttcttaaatgtgtatattttctttgaatagtatatgctgaatctatcaagttcgaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTCGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
||| |      || ||  |  || |  |||| |        || ||  | | ||||  |||| ||  ||          |  ||||    |||||||| ||  || |||| ||||| |||||||  |||||| ||||||| ||  | ||||| || |||||||||||||| || ||||||||||||||||| ||||
gtaagagacacttcttcttctgtttcttttgatttgatcacttgtt--gttttctg--aatgtgttcctgc--------ttgttgc--aattgcagGCTGAGATTAATTTCCTTGGTAACCTTCTCCATCCAAATCTAGTTAAGCTTGTTGGTTATTGCATTGAAGATGATCAAAGGTTGCTTGTGTATGAGTTTA

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|32938653|gb|CF043472.1|CF043472
EST:     ATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: ATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|6021366|gb|AW066294.1|AW066294
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|32938832|gb|CF043651.1|CF043651
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|71595774|gb|DR906525.1|DR906525
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|7238071|gb|AW573443.1|AW573443
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|50323063|gb|CO518189.1|CO518189
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|211053378|gb|FL364311.1|FL364311
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
EST: gi|19436855|gb|BM953265.1|BM953265
EST:     CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTG                         GCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG
genomic: CTGTCAAGACACTCAACCATGATGGGTTGCAGGGGCATAAAGAGTGGGTGgtatgttttt ... ttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
             tgctaat  putative branch site (score: 2)
                                            cttgttt  putative PPT
                                aaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG