Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTTATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgctgacttacatcctgttcttagtaaaaatatgtggtgtttattttagcttaaattgaaatccatctcttactggaatgagattagaagtgt...

Basic information

species Oryza sativa
transcript LOC_Os08g41250.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G015642_T01 (Zea mays), 5'ss of exon 5
GGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTTATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgctgacttacatcctg-ttcttagtaaaaatatgtggtgtttattttagcttaaattgaaatccatctcttactggaatgagattagaagtgt-
||||||| ||||| |||||||||||||||||| |||| |||||  | || | | ||||||||||||| ||||||||||||| |||||| ||||||||||||||| ||   || |     |  |  || |||| ||| |    |||||| ||||| | ||  | ||  | |     |  |  |    ||| ||||  ||||| 
GGCTCAAGCCCAAGCTTGATGAAGTCCTGCCTAAAGCTGCTGGGGTTGTCTTTATTGTTGATGCTCAGGATTTCTTGTCTAGCATGCAAGCTGCTGCAGAgtaaattttgtgccccctgttttactttttagcaaatactattggtgtctatttcatct--acttttactgtcctttgtggtaagttgaaattaacagtgta

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G091503_T04 (Zea mays), 5'ss of exon 5
GGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTTATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaa-tttcgctgacttacatcct--gttcttagtaaaaatatgtggtgtttattttagcttaaattgaaatccatctcttactggaatgagattagaagtgt
|||||||||||||||||||||||||||||||| |||| ||||   | || | ||||||||||||||||||||||||||||| |||||| ||||||||||||||| ||| ||       | ||||   || |||  |||   || |||||| |||||    || | |  |  | ||  |     ||   | || ||| |  |  
GGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCTTTGTTGTTGATGCTCAAGATTTCTTGTCTAGCATGCAAGCTGCTGCAGAgtaaattttgcccctccccttccttaatttttaccaaatgcatttggtgtctatttctatttca-tctactttcactttcctttgtgctaagttta-agtta-
















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|89179899|gb|CI044178.1|CI044178
EST:     CCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: CCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|66914691|gb|CX101539.1|CX101539
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88238107|gb|CI237956.1|CI237956
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88991856|gb|CI034994.1|CI034994
EST:     TTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|163925831|gb|EG709627.1|EG709627
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|86855157|gb|CI263224.1|CI263224
EST:     ATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: ATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|86595517|gb|CI264614.1|CI264614
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|4879170|gb|AU063469.1|AU063469
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|33685925|gb|CF314164.1|CF314164
EST:     TATGTTGTTGATGCTCAAGATTTTTTGTTTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|86594321|gb|CI251193.1|CI251193
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88217759|gb|CI217608.1|CI217608
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88903705|gb|CI089243.1|CI089243
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88524868|gb|CI453822.1|CI453822
EST:     CATGCATGCTGGTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: CATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|3760359|gb|C97613.1|C97613
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTNTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|33685924|gb|CF314163.1|CF314163
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|86414979|gb|CI069382.1|CI069382
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|11118086|gb|AU163274.1|AU163274
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|86511780|gb|CI154413.1|CI154413
EST:     TCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|15858404|gb|BI811216.1|BI811216
EST:     GTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: GTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|88206590|gb|CI206439.1|CI206439
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|10931045|gb|AU161319.1|AU161319
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
EST: gi|218481364|gb|FG954015.1|FG954015
EST:     TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGA                         GTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC
genomic: TATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgc ... ctttccgcagGTACTTGTATGACATCCTGACAAAGGCAACTGTAGTGAAGAAGAGGGTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTTATGTTGTTGATGCTCAAGATTTCTTGTCTACCATGCATGCTGCTGCAGAgtaatttcgctgacttacatcctgttcttagtaaaaatatgtggtgtttattttagcttaaattgaaatccatctcttactggaatgagattagaagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata