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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatctgattcacatctttgtttcaatctcttgttctgtttctggtaaattgaatcaacggtgttgatttttgcccag

Basic information

species Arabidopsis thaliana
transcript AT1G01720.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 5'ss of exon 2
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatg---gaatcagatctgat-tcacatctttgtttcaatctcttgttctgtttctg--------gtaaattgaatcaacggtgttgatttttgcccag
|||||| || || ||||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||| |||| ||||||||||| || ||||||||| | || || | | | | |||| | | || || ||||| | | ||| | | | | | || |||||
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAA---CAGCCTCAGGgtaagcaaaaaccacacccaagattccatcactaaattcattactaaatctgtgttcatcgtgattattgattaatttagtcacctaattattcgcccaa

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 5'ss of exon 1
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAAT-----AGTCTCAGGgtatggaatcagat--ctgattcacatctttgtttcaatc-tcttgttctgtttctggtaaattgaatcaacggt--gttgatttttgcccag
|||||| || || ||||| || || ||||| |||||||||||||||||||| ||||||||||| ||||| |||| ||||||||||| | || || | || | | | || || | || | || || ||| ||| | |||| | | || | | ||| | | |
CGCCGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAACACCCTCCGGgtacatatatacgccattaattaattacctcgaatttgctcttaattcatcaaattcaaattcagacgaattctactctcagttaatcaagtttagacaa-

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 5'ss of exon 2
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCG------TTCGCAAG------AAGA------AGAATAGTCTCAGGgtatggaatcagatct--gattcacatctttgtttcaatctcttgttctgtttctggtaaat-tgaatcaacggtgttgatttttgcccag---------
| || ||||| |||||||||||||||||||| ||||||||||| ||||| |||| |||||| ||| | || |||||||| | | | | ||| | | || | || | ||||| | ||| || || || | || | || ||| |||
------------------CGTCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCGCCGCCCGCAAGCTCTCCAAGTCCTCCCACAACGCCCTCAGGgttagtatttacttcttttaattacttacttctcctaatctaatcatctcttgctttcaatcatttctcctcaccaacgaatttacccccattttatttt

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G014653_T02 (Zea mays), 5'ss of exon 1
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAA---TAGTCTCAGGgtatggaatcagatctgattcacatctttgtttcaatc-tcttgttctgtttctggtaaattgaa-tcaacggtgttgatttttgcccag----
|||||| || || ||||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||| || | ||||||||||| | || | || | | || | | | | ||| || || || || ||| ||| | || | || | |
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCGGCGCGCAAGAAGAACAGCCTCAGGgtaagaacaagcgctccgccgccgtccgtccgtccgttggcgtcgtcaccgtccaaatcaaacaaaaagaacttggcgataatgtgtcgctttcgtaatg

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G180328_T01 (Zea mays), 5'ss of exon 2
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatg--------gaatcagatctgattcacatctttgtttcaatctcttgttctgtttctg----gtaaattgaatc--aacggtgttgatttttgcccag
|||||| || || ||||| || || ||||| ||||||||||| |||||||| ||||||||||| ||||| ||| ||||||||||| || || ||||||||| | || || || | | | ||| ||| ||| ||||||| | ||||| || || | ||| ||
CGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCATGAGTACCGCCTCGCCGACGTCGACCGCACCGCCCGCAAGAAGAACAACAGCCTCAGGgtacgttgcgatcgatcgagttccggccggcgcgtccaccagaatatctcattc-gtttctgtgcagaaaattatctcttgctcgtatatattattatttg-

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G123667_T03 (Zea mays), 5'ss of exon 2
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGT------CCGTTCGCAAGAAGAAGAATAGT---CTCAGGgtatggaatcagatc-tgattcacatctttgtttca-atctcttgttctgt--ttctggtaaattgaatcaacggtgttgatttttgcccag--------
|| ||||| | || ||||| |||||||||||||||||||| ||||| ||||| ||||| | ||| |||||||||| || | ||||||||| | | | | ||| || || || | | | | | ||| | | | | | || | | | |
---------GCCCAAGGGCGTCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCGGACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGGgtaattcactacaccatgacctttctcaggagaacatatttatctccccgaaatactgacacttgcagttagagggaaaaaatatagagagaagtaaaaa

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA14G24220.1 (Glycine max), 5'ss of exon 2
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatctgattcacat--------ctttgtttcaatctcttgttctgtttctggtaaattgaatcaacggtgttgatttttgcccag----
|| ||||| || |||||||||||||| || ||||||||||||||||| ||||| || ||||| || || ||||||||||| ||||| || | ||||||| | ||| | || | | | || || || | | | ||| || || || |||| ||
CGCTGGAAAAGCGCCCAAGGGAGAGAAAACTAACTGGATCATGCACGAGTATCGTCTTGCAGACGTGGATCGTTCCGTTCGCAAAAAGAA---CAGCTTAAGGgtatattcccctttctctcttcaatacgaaggacataatggacatttcgtggcacaaatattacctttcgaaatcaccgttttacttttacccttaaata

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 2
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGA-----ATAGTCT-CAGGgtatggaatcagatctgattcac-atctttgtttcaatctcttgttctgtttctg-------gtaaattgaatcaacggtgttgatttttgcccag
|| |||||||| || || || |||| ||||||||||||||||||||| |||||||| ||||| || || ||||||||||| ||||| | | || | | | | | | ||| |||| || ||| | || | | ||| || | ||| | | |||||| |
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg-----

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G26480.1 (Glycine max), 5'ss of exon 2
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatctga---ttcacatctttgtt-tcaatctcttgttc--tgtttctg-gtaaattgaatcaacggtgttgat--ttttgcccag---
||| ||||| || ||||||| |||||| || ||||||||||||||||| |||||||||||||| || || || |||||||| ||||| || | ||||||| | || | || |||| | || | | | | |||| | | ||| | || | | |||| |||
CGCCGGAAAAGCGCCCAAGGGAGTGAAAACTAACTGGATCATGCACGAGTATCGTCTCGCCGACGTGGATCGTTCGGTTCGCAAAAAGAA---CAGCTTAAGGgtatataccagtatgcgcccttttttctcttcactatcgaggacataatagacatttcaacgcacatttacctttcgaaaatcaccgttttaccctttaa

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatc--tgatt-cacatctttgtttcaatctcttgtt-ctgtttctggtaaattgaatcaacggtgttgatttttgcccag---------
|| |||||||| || || || || | ||||||||||||||||||||| ||||||||||| || || || ||||||||||| ||||| || || |||||| | | || |||| ||| || | | || | || ||||| || || | ||| | ||
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAA---CAGCCTAAGGgtacatacatacatgaatgatgatgcatgccctttctagttcaagattattaggataggataattgcatgaa-attacgactttgccctcaagttgaagct

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0001g02300.t01 (Vitis vinifera), 5'ss of exon 2
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatca-gatctgattcacatctttgtttcaatctcttgttctgtttctggtaaattgaatcaacggtgttgatttttgcccag-------------
||| ||||| || | ||||||||| || |||||||| ||||| || ||||| || || ||||| |||||||| | |||||||||||| ||||| | |||||| | | || | | ||||| | | ||| || | ||| | |||| || ||| || ||| || | |
CGGAAAAGCCCCCAGGGGAGAGAAGACAAATTGGATTATGCATGAATACCGGCTGGCAGACGTGGACCGGTCGGCTCGCAAGAAGAATAATAGCTTAAGGgtacttagccttgaaccgcttcaccaatat-tttagggctaaaatgggctttttaataaaaatcatgaaccgt-cagatcttggactgaatacttagtttga

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S164_25V6.1 (Physcomitrella patens), 5'ss of exon 3
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGG---TCCGTTCGCAAGA---AGAAGAATAGTCTCAGGgtatggaatcagatct---gattcacat-ctttgtttcaatctcttgtt-----ctgtttctggtaaattgaatcaacggtgttgatttttgcccag-----------------------------------------------------------------------------
||| |||||||| |||||||| || ||||||||||||||||| || ||||| || | || | | ||| || | | ||| | | ||||| || || |||||| | | | |||| || |||||| || || || | | | | | || || |
------AGCACCAAAGGGCGAGAAAACGAACTGGATCATGCACGAGTATCGCCTCGCTGAAGGTGTCTCGACCTCCACTCATCATCCTCGAAGGAACTCTTCGCGAgtatgtcctccattcccccacctcacatgcactaccgttaggtcttattaaaggctgtttatgagaatttaggaccaggttttcgaagttgaacttctagggtttctgagaacatgtccaacgtagtctcgagaattttcctcctcaccttttgactaaattttggtaatgcag

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCC---GTTCGCAAGAAGAAGAATAGTCTCA---GGgtatggaat---cagatctgattcacatctttgtttcaatctcttgttct-----gtttctggtaaat--tgaatcaacg-gtgttgatttttgcccag--------------------------------
|| || ||||| ||||||||||| ||||||||||||||||| || || || || | | | || | || | | | | | ||||||| | | |||| | ||| | | || || | | || ||| | | | | |||||| | ||||| | | | ||||
------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ38403 (Selaginella moellendorffii), 5'ss of exon 1
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACC-----GGTCCGTTCGCAAGAAGAAGAATAGT-CTCAGGgtatggaatcagatctgattcacatctttgtttcaatctcttgttctgtttctggtaaattgaatcaacggtgttgatttttgcccag
|||||||||||| | ||| |||| ||||| ||||||||||||||||||| || || | || ||||| || | || | || |||| || || | | |||| | | || || | || | | ||||| | ||| | |
------AGCTCCAAAGGGCGTCAAATCCAACTGGATAATGCACGAGTACCGTCTCGTGGATCCAAACAACAAGGCTCTCTTCGCCAGGAAGCGAGGATCACTGCGGgtttgaaagccg--ctgact-agatgttgact---ggctttgactatgtttgacttccatttttttcag-------------------

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ20531 (Selaginella moellendorffii), 5'ss of exon 1
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGA---CGTTGACCGGTCCGTT----------------CGCAAGAAGAAGAATAGTCTCAGGgtatggaa----tcagatctgattcacatctttgtttcaatctcttgttctgtttctggtaaa----ttgaatcaacggtgt------tgatttttgcccag
| || || ||||||||||||||||||||||| |||||||| | | | | ||| || | ||| || | ||||||||| | | || | | || | | ||| | ||||| | ||| |||| || | || | |||| | || ||||
------------------ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGATAGCAGCGCCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCG-CTCAGGgtaagaagaatctccgtcatcgcctcagtcatggcttc--tttcttgcattctttgtggtgaaatcctcgatttcctggtgaaattcgcgtttcttgcttga

upper sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ28600 (Selaginella moellendorffii), 5'ss of exon 1
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGA---CGTTGACCGGTCCGTT----------------CGCAAGAAGAAGAATAGTCTCAGGgtatggaa----tcagatctgattcacatctttgtttcaatctcttgttctgtttctggtaaa----ttgaatcaacggtgt------tgatttttgcccag
| || || ||||||||||||||||||||||| |||||||| | | | | ||| || | ||| || | ||||||||| | | || | | || | | ||| | ||||| | ||| |||| || | || | |||| | || ||||
------------------ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGATAGCAGCGCCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCG-CTCAGGgtaagaagaatctccgccatcgcctcggtcatggcttc--tttcttgcattctttgtggtgaaatcctcgatttcctggtgaaattcgcgtttcttgcttga

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|301501784|gb|HO207324.1|HO207324
EST:     GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGG                         CTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
genomic: GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatc ... ttttgcccagCTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
EST: gi|125073546|gb|EL137838.1|EL137838
EST:     AAGAATAGTCTCAGG                         CTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
genomic: AAGAATAGTCTCAGGgtatggaatc ... ttttgcccagCTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
EST: gi|301502474|gb|HO208014.1|HO208014
EST:     GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGG                         CTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
genomic: GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatc ... ttttgcccagCTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
EST: gi|301501314|gb|HO206854.1|HO206854
EST:     GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGG                         CTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
genomic: GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatc ... ttttgcccagCTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAG
EST: gi|116443557|gb|EG486149.1|EG486149
EST:     GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGG                         CTGGATGATTGGGTTCTCTGCCGGATTTAC
genomic: GTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatc ... ttttgcccagCTGGATGATTGGGTTCTCTGCCGGATTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatctgattcacatctttgtttcaatctcttgttctgtttctggtaaattgaatcaacggtgttgatttttgcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG