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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcacctattttcttttcctgctgtaatgtgatgggaaaaaaag

Basic information

species Zea mays
transcript GRMZM2G014116_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 8
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcac-ctattttcttttcctgctgtaatgtgatgggaaaaaaag
|||||||||| |||||| | || ||||||||||| ||||||||||||||||||||||| ||||| || || ||||| || || || || ||||||||| |||||  | ||| || |||||  |||   | ||| || |         |||||   | |||| ||   ||| || ||  |  ||||||  |  |||||||| |    
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgt-tgctttcaggatta--caaattatcat--------ggttt---ttaatgttctttctaattcctacttttgctgt--ttggatgggaatag---

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 8
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcacctattttcttttcctgctgtaatgtgatgggaaaaaaag
| |||||||||||||| ||||| ||  ||||||| ||||| ||||||||||||||| | ||  | |||||||| ||  | || || || ||||| |||| |||   | |      ||| |   |    |  ||   || || | ||   ||| ||| |    |  | | |  | |  |    |||| || || || |   |    
TATGTTGGTACTTGGTTCTAGCGCCCTATGATCCAATGCAGTCAAGCCTTCTCAATTCCACCTTGGAGGATAAGAATATATCTGAGATTCCAAACTTCAAgtatgttatcctaactttta---tctcacgtattccaagtc-atgttcattt-tcttaggatttccttgtcatttggtgtgcctgttatatgttgtgcctag---

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 8
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcacctattttcttttcctgctgtaatgtgatgggaaaaaaag
| |||||||||||||| ||||| ||  ||||||| |||||||||||| |||||||| | ||  | | |||||| || || || || || ||||| |||| |||   |||      ||| |       | |   ||      || ||   ||| | | |    |  | | |  | |  |    |||| || || || |   |    
TATGTTGGTACTTGGTTCTAGCGCCCTATGATCCAATGCAATCAAGCTTTCTCAATTCCACCTTGGCGGATAAGAATCTATCTGAGATTCCAAACTTCAAgtatgttctcctaacttttatcccatgttttccaag----tcacgttcatttgttt-aggatttccttgtcatttggtgtacctgttatatg-tgtgcctag---

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 8
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcacctattttcttttcctgctgtaatgtgatgggaaaaaaag
| |||||||| ||||| ||| |||| |||||||| ||||| ||||||||||||||| ||||  | |||||||| || || || || || ||||| || | ||||  |||   |  | |  || |||      |  | |       | | | |   |   |  |||  |  |  |  |      | | |||  || |         
TATGTTGGTATTTGGTTCTATCACCGCATGATCCAATGCAGTCAAGCCTTCTCAATTCTACCTTGGAGGATAAGAATCTGTCTGAGATTCCAAACTTTAAgtacg-tcttcctaatcttgaagttgcgtgtcttgttagatgttttagttatgctttccttctcatttgatgcccctgttatttatcatgccatag---------

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|31910182|gb|CD651296.1|CD651296
EST:     CTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|113701567|gb|EE679071.1|EE679071
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|24769954|gb|CA405083.1|CA405083
EST:     AATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: AATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|211388540|gb|FL326080.1|FL326080
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|453340|gb|T15314.1|T15314
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|60343636|gb|DN210609.1|DN210609
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|60341988|gb|DN208961.1|DN208961
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|60344719|gb|DN211692.1|DN211692
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|211150173|gb|FL276378.1|FL276378
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|24766335|gb|CA401489.1|CA401489
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|32907838|gb|CF012651.1|CF012651
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAATCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|211150172|gb|FL276377.1|FL276377
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGGAAGCAGCTGGCCACCCATGGAGGTGATACAGTGGGACAAG
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTG-AAGCAGCTGGTCACC-ATGGAGGTGATACAGTGG-ACAAG
EST: gi|16379510|gb|BI992995.1|BI992995
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|71762659|gb|DR960596.1|DR960596
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|60346799|gb|DN213772.1|DN213772
EST:     AGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: AGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|16926500|gb|BM079573.1|BM079573
EST:     CAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: CAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
EST: gi|26457612|gb|CA829195.1|CA829195
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATA
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATA
EST: gi|24764505|gb|CA399669.1|CA399669
EST:     AGAAATCCCAAATTTCAG                         GTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT
genomic: AGAAATCCCAAATTTCAGgtacaatctg ... ggaaaaaaagGTTATTACTGAAGCAGCTGGTCACCATGGAGGTGATACAGTGGACAAGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcacctattttcttttcctgctgtaatgtgatgggaaaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT