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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttcgacttactaatcactcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag

Basic information

species Arabidopsis thaliana
transcript AT4G25740.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25740.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 5'ss of exon 4
AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACGTGG---TGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttcgacttactaatcactcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag
     ||  ||||  |||  |||||| |||    ||||| |  ||  |||    ||||| |||||||||||||||||| ||||| |||||||| || ||    ||||         || |  |  | |  |   ||| ||  |   | || | |  |    || ||    | |  |   |||    ||||     |    ||| ||  ||                                               
---TGGTGACAGAGATGGGTACCGTGGTGGTCCTCGTGGTGCTCCTGGTGACTTTGGTGGTGAGAAGGGTGGAGCTCCTGCTGAGTTCCAGCCATCCTTTAGGgtaatcaactactttccctacaagtgtttcattattgttctgttgtgtcatgta---gcttatttgacttgttacgctg----aatacaagacaagcaaaatccatt-----------------------------------------------

upper sequence: AT4G25740.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g73160.1 (Oryza sativa), 5'ss of exon 4
AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACGTGGT---GGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttcgacttactaatcac-tcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag
     ||  |||   |||| || | | |||    ||||| |  ||| ||| |   ||||  ||||||||||| ||||||||||| |||||||| |||||    ||||    || | | || |    | | |   | | |     |||  | | | |     |||  |||    || || | ||    ||||       |||  |   ||| |                                              
---TGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAGGGTGGTGCTCCAGCTGAGTTCCAGCCATCTTTTAGGgtaagagctctaatgaccatctgcatacctatatgccattgctaggttcatccag---actgctcatagataatttattggcttaata------atttggaacatttga----------------------------------------------

upper sequence: AT4G25740.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G02410.1 (Glycine max), 5'ss of exon 4
AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACG------TGGTGGTGAT------GAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttcgacttactaatcactcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag
               ||||||||||||||||||||||||||| |||||      ||||||||||      || |||||||||||||| ||||| | |  ||| |||||    ||||   ||   |  |   |||| |     ||   ||   ||||     ||| |  ||  ||||| |  || |    |||  | || || ||  ||||  || |  ||  || |                                        
------------CGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGTGGAGCTCCTGCTGACTACAGGCCTTCTTTTGGGgtaagctttttgca-atatatcaattaacattatttg---ctat---tattcta--tatcaatcaatattattg---tgtttctatttgttt-atttattgtttgcta-ttatt----------------------------------------

upper sequence: AT4G25740.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G43110.1 (Glycine max), 5'ss of exon 4
AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACG------TGGTGGTGAT------GAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatctt---cgacttactaatcactcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag
                |||||||||||||||||||||||||| |||||      ||| ||||||      || |||||||||||||| ||||| | |  ||| |||||    |||| | ||   | |  ||  |||||    ||  ||| ||    | |||   ||    ||| |  |  ||  || ||   | ||  ||    |||   ||  |                                                      
------------CGGCGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGCGGTGATTTCGGTGACAAGGGTGGAGCTCCTGCTGACTACAGGCCTTCTTTTGGGgtaagttttttgcaatatatcaatcaacatta--ttattgtctttctatttgtttgttttattgtttgcttttattttg-tatgttaactatcttttcttgta------------------------------------------------------

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|86053964|gb|DR349721.1|DR349721
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTA
EST: gi|86075921|gb|DR371678.1|DR371678
EST:     GTGGTGATGAGAAGAGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|86053989|gb|DR349746.1|DR349746
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGNTTTCCAGCCGTCTTTCCAA                         GGATGTGGTGGTAGG
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGG
EST: gi|164230430|gb|ES046615.1|ES046615
EST:     GAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTG-CCGTGGTGCAGG
genomic: GAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGG
EST: gi|124891756|gb|EH970658.1|EH970658
EST:     CTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: CTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|86081565|gb|DR377322.1|DR377322
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|86053952|gb|DR349709.1|DR349709
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|47828785|gb|CK118469.1|CK118469
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|86053950|gb|DR349707.1|DR349707
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|47828802|gb|CK118486.1|CK118486
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCA-                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|47828506|gb|CK118190.1|CK118190
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTG
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTG
EST: gi|164192833|gb|EL981740.1|EL981740
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCG
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCG
EST: gi|125260730|gb|EL274815.1|EL274815
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGG
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGG
EST: gi|125242262|gb|EL256347.1|EL256347
EST:     TGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAG
genomic: TGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAG
EST: gi|86053969|gb|DR349726.1|DR349726
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTACAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|47831509|gb|CK121193.1|CK121193
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
EST: gi|86082367|gb|DR378126.1|DR378126
EST:     GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA                         GGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA
genomic: GTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttc ... atgttggcagGGAGGTGGTGGTAGGCCTGGTTTTGGCCGTGGTGCAGGCGGTTACAGTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAAgtaaatcttcgacttactaatcactcctagtttactgagcctatatgccttccacttactaatcactcctagttaactgtgccaatatgcttcgtttaaagtcttttagctagttgatgaagagattgtctaacagcgtgttgtatgttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT