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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttgctaccaagttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

Basic information

species Arabidopsis thaliana
transcript AT4G38510.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtttgtttttgctaccaagttttaaagtatcagtg--tctataatat--actcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                       |||| | | |  | ||  ||||  | ||| || ||          ||    | | || |       || |||| ||||||  ||||||||||||| ||  | ||||||||||| ||||| || ||||| || || || |||||||| || || |||||||| ||||| ||||| ||||
tgaataatctataagtttttgtagtttatatctttt-ccttgtttgcatgtagcactgaagtagcggcattgcttaatatgtgtggtaattctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
--------------------------gtttgtttttgctaccaagtt--ttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                          |||| | |||  ||||  |||  || |   ||     |||    |      ||| |      ||||| ||  | ||||||||||||||||||| ||  | ||||||||||| ||||| || |||||||| || || || |||||||| || || || |||||||| || || ||||
accaggttaaatttaacaatgatattgttt-tctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattg-tgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
---------------------------gtttgtttttgctaccaagttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                           |||| | ||   ||||  ||||      |  |   | | |  | |  | |     | || ||| |||   | ||||||||||||||||||| ||  | ||||||||||| ||||| || |||||||| || || || |||||||| || || || ||||| ||||| || ||||
tctggcagtgggtctgccctttttagtgttt-tcttcattaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
-------------------------gtttgtttttgctaccaagttttaaagtatcagt-gtctataatatactcacattttccaatgttttt-tccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                         | ||||||    | |   | || |   || | || | ||   || |  |  | |     | ||||||| | || |||| || |||||||| || || ||||| |||||||| ||||| ||||||||||| || || || ||||| || |||||||| ||||| || ||||| ||||
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttc-tcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 5
---------------------gtttgtttttgctaccaagttttaa--agtatcagtgtcta-taatatactcacattttccaatgttttt-tccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT-
                      |||| || |   |    |||| ||  ||| | | |||  | |   ||  |  | ||    | ||||||| | || |||| || |||||||| || || ||||| |||||||| ||||| ||||||||||| || || || ||||| || |||||||| || || |||||||| |||| 
tgattattgaatcctttttcattttgattctttgattttgtttgaatcagtttaactgttgactcccattttttccttaattattgtttttgttcacaggTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
----------gtttgtttttgctaccaagttttaaagtatcagtgtc--tataatatac---------tcacattttccaatgttttt-----tccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
            ||  |||| |     | |||||  ||||  |  ||  | || |  ||         ||   ||||||  | |||||     |||| |||| || ||||||||||| ||  |||| |||||||| ||||| || |||||||| || || || ||||| || |||||||| || || |||||||| ||| 
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtttgtttttgctaccaagtt----ttaaagtatcagtgtctata-atatactcacattttccaatgtt---ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                     | | | |  || ||  ||    | ||  | |   | ||| || ||||       | | ||  | ||    |||  | ||||||||||||||||||| || |||||||||||||| || ||||| |||||||||||||| |||||||| || || || ||||||||||| ||||| ||||
gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------gtttgtttttgctaccaa-----gttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                       |||   ||   ||         || || |  | |   | |   ||||  | | | ||||       ||  |    |||||  | ||||| || || || ||||| |||||||| || |||||||||||||| ||||| |||||||||||||| || || ||  |  | || || ||| 
ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatg-atttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

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|86066803|gb|DR362560.1|DR362560
EST:     GAACATCTGGAATCGACAACAAGTACACAACTGNGNAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGG
genomic: GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGG
EST: gi|125194242|gb|EL209196.1|EL209196
EST:     CAACTGTGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
genomic: CAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
EST: gi|125252985|gb|EL267070.1|EL267070
EST:     TCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
genomic: TCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
EST: gi|86066806|gb|DR362563.1|DR362563
EST:     GAACATCTGGAATCGACAACAAGTACACAACTGNGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
genomic: GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
EST: gi|125076187|gb|EL139433.1|EL139433
EST:     GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGC
genomic: GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGC
EST: gi|164219463|gb|ES051039.1|ES051039
EST:     TCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG                         GTTTTG-AAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
genomic: TCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
EST: gi|86066801|gb|DR362558.1|DR362558
EST:     GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
genomic: GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGT
EST: gi|125284482|gb|EL298567.1|EL298567
EST:     GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG                         GTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTC
genomic: GAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAGgtttgttttt ... ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT
                         tactcac  putative branch site (score: 1)
                                         tgttttttcc  putative PPT
                tctataatata  TA-rich tract