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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgctactgctattttttttttcatgatttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT

Basic information

species Oryza sativa
transcript LOC_Os04g41100.6
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 5
gtaatgtgctactgctattttttttttcatgatttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
     |||| |||  || | |    |      || ||||  |  ||| ||  | |       || ||||||||||| |||||    | |||||||  |||||||||| | |||| || | ||  | ||||||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| |||||| 
-----gtgcaacttttactctcaaatcggcatttgatattct-tatt-atcatcattcgtaccagtctgagcacacttgtttctcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAAC

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G179097_T08 (Zea mays), 3'ss of exon 5
gtaatgtgctactgctattttttttttcatg-atttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
     ||||   |  || |    ||   ||   ||| ||   |    | ||  | |   |   ||  |||||||||| | |||      |||||||  |||||||||| | |||| |  ||||  | ||||||  |||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||| 
-----gtgcagtttttactcaaattggtatttgtttttagatttttattatcatcatgcataccagactgagcacacttttttctctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAAC

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G10810.1 (Glycine max), 3'ss of exon 4
gtaatgtgctactgctattttttttttcatgatttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
|||| | | |||      |   |   | |   ||  || ||   |||  | | | |||| |  ||| | ||  |  || ||||     | |||||| |  | || || | |||| |  | |||||||||||||||||||||||||| || |||   || || |||||||| ||||| ||||||| | |||   
gtaaag-gttacatgagctacatgaatta-atttggtaacaaatatt--tgtctgaatatt--aatgtaagacctactatttta----tgcagCGGATCACTGCCGAAGATGCTCTAAATCATGAGTGGTTCCGTGAAGTTCCTCTCCCCAAAAGTAAAGAATTCATGCCTACATTTCCTGCTCAACATGCTC

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G67580.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgtgctactgctattttttttttcatg-atttatatcatgcattcatatttaa-atacttcaatctgagcacacctgttttggctt-tacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
|||||     |    ||| | ||    |||| || |  |||  | || ||  || |   | | |  |  |  | |   ||||     ||| | ||| |  || | |   |||  ||| |  ||||||| |||||||| ||||| ||||| || ||||| || ||||||||||| || || ||||||| | |||   
gtaatagaaaatatatatctgttg---catgcatgttaatccagtatgcaccttaattgttccttgacttttggatctctgtggcttcttctgcagAGAATAACTGTTAATGAAGCTCTAAAGCATGATTGGTTCCGCGAAGTCCCTCTGCCAAAATCCAAAGATTTCATGCCTACTTTTCCTGCTCAACATGCCC

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 3'ss of exon 4
------gtaatgtgctactgctattttttttttcatga-----tttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggct-ttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
       |   || | ||  ||||   | |||| | ||     ||| | |  |   ||  |||||| ||| |    | |       ||| | |   || |||||| || |  |||| || |||||| |  | ||||| |||||||| ||||||||||| || ||||| || ||||||||||| || || |||||||   |||   
gtgattttttagttcaacatctataaatgttttgaggaaatgttttgttttctaggttggtatttagataatgttgtttattatggcctttatgttctattacagAGGATTACAGCTGAAGCTGCTCTTAACCATGATTGGTTCCGCGAAGTTCCTCTTCCCAAATCTAAAGATTTCATGCCTACTTTTCCTGCTCAGCATGCCC

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|29677523|gb|CB673798.1|CB673798
EST:     CAGGTTTTGATCTGTTAAATAATCTTTTAACATGCGATCCTGGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCC
genomic: CAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCT-GAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCC
EST: gi|29679249|gb|CB675524.1|CB675524
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|218494622|gb|FG958132.1|FG958132
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|66913038|gb|CX099886.1|CX099886
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29638284|gb|CB643293.1|CB643293
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29670899|gb|CB667174.1|CB667174
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|18385570|gb|BM418769.1|BM418769
EST:     CTTCGTAACATACGATCCTGGAGAA-                         CGGTTATCAGCAGAT-CTGC-TTGCAGCATGAGTGGTTCCGTGAAGTTCC
genomic: CTTC-TAACATACGATCCT-GAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCC
EST: gi|29630958|gb|CB635967.1|CB635967
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|86910572|gb|CI294713.1|CI294713
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29672610|gb|CB668885.1|CB668885
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29674831|gb|CB671106.1|CB671106
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|58611941|gb|CK039653.1|CK039653
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTGTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29638205|gb|CB643214.1|CB643214
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29629173|gb|CB634184.1|CB634184
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|86479976|gb|CI122609.1|CI122609
EST:     TCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: TCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|58607487|gb|CK035520.1|CK035520
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
EST: gi|29640025|gb|CB645034.1|CB645034
EST:     AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAG                         CGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT
genomic: AAGCAGGTTTTGATCTGTTAAATAATCTTCTAACATACGATCCTGAGAAGgtaatgtgct ... ggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT
      attcatatttaaatac  TA-rich tract