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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattgactgcctcaagtcaattgtactctgaagagaaggaaaaaatctgttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------gtgagcattgactgcctcaagtcaattgtactctgaagagaaggaaaaaatctgt---tttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                                                 |||    ||   |   |||   |   ||    || ||   |         ||||    | | |||  | ||   ||||  || ||  |||||||||||| || ||||||||||||||||| || ||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||| || || ||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttt-tatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------gtgagcattgactgcctcaagtcaattg-tactctgaagagaaggaaaaaatctgt-tttaaattgtttcggtcgata-----atttt--tatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                                                             | |||  |   |  | |     |||| |    |||    ||  ||  | ||  | |||||||| | |   |   ||     |||||  |  ||||||||| || ||||||||||| |||||||| || || |||||||| ||||| ||||| || ||||||||||||||||| ||||||||||||||||| ||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------gtgagcattgactgcctcaagtcaattgtactctgaagagaaggaaaaaatct-----gttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                                                                    ||  |  ||    |  |  | | | | |     | ||   || ||    ||||     ||||  |||  | |     |||  || ||  ||||||||| || || |||||||| |||||||| || || |||||||| ||||| ||||| || ||||||||||| |||||||||||||||||||| || ||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgatt-ttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
gtgagcattgactgcctca-agtcaattgtactctgaagagaaggaaaaaatct-----------gttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
|| || | ||   |    | | | | || |   |  |||  | |||||| || |           | | || | |       ||  |   ||| ||||||||||| |||||||||||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| || || ||
gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataataaactcttccttgtctttcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gtgagcattgactgcct-caagtcaattgtactctgaagagaaggaaaaaatctgtt--ttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                            | | |  | |||| || |||     | | |   |       | |||    | | ||  |||||  || |   | |||  |   |  |||   |||||||||||| |||||  | || |||||||| |||||||| ||||| || || ||||||||||||||||||||||| |||||||| || || ||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtct-acttgatg-tggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtgagcattgactgcctcaagtcaattgtactctgaagagaaggaaaaaatctgttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                    |   || | ||  |  ||  |      || | |  | |||  ||| | || || ||   |||  |    | || | |      |||   ||| ||||| || |||||| | || || ||||| |||||||| || || || || ||||| |||||||||||||||||||| ||| | ||||| ||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttgga-atattttttaaagattgaagagatttgctt---attagtcaatttgaca-tgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------gtgagc-attgactgcctcaagtcaattgtactctgaagagaa----ggaaaaaatctgttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                          | | | | |  |   || |  ||| |  ||   || ||    | |  |||| ||||| | ||| | |   |||||  |  | | |||    || ||||| || |||||  | || ||||| || |||||||| ||||| || || ||||| ||||||||||||||||| |||||||| || || ||
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatat---tcgatc-tgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

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|116471926|gb|EG514518.1|EG514518
EST:     AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGGTGATACAAA
genomic: AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattg ... atttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
EST: gi|116483049|gb|EG525641.1|EG525641
EST:     AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
genomic: AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattg ... atttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
EST: gi|164195239|gb|EL968704.1|EL968704
EST:     TTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
genomic: TTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattg ... atttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
EST: gi|116424900|gb|EG467492.1|EG467492
EST:     AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTG                         GAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
genomic: AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattg ... atttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAA
EST: gi|152038085|gb|BP807684.2|BP807684
EST:     AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATAC-TTGATATTTCTG                         GAAGT-CAATCAACCCCAGTGAAAG
genomic: AATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattg ... atttttatagGAAGTTCAATCAACCCCAGTGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaagagaaggaaaaaatctgttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA
                                              tttttat  CT-rich tract
             aaaaaatctgttttaa  TA-rich tract