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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaacatatctccttttgaccatccttatacattggtgtttgttttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT

Basic information

species Arabidopsis thaliana
transcript AT1G64680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G175989_T01 (Zea mays), 3'ss of exon 1
gtatgtaacatatctccttttgaccatccttatacattggtgtttgttttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT
||  ||    | |||   | | |  || |         |||| |      |||        |  ||||       || |||||  ||||||||||||||||||||||||||||| || |  || ||  | || || |||||    ||  | |||||| ||||     |     | |
gtgagtgctctgtctggctct-attattcaggggagcgggtgatgaa---catggattgattggccatccg----tgcagATTTCGAAGACATGAGCTGCGAGATGATATACGGCCAGGTGCCGCCTCCGTTGGAAGAGGACCCGGCGTCGAAGCAAGCTTGCTACCCGAGCCTCT

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25185 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtaacatatctccttttgaccatccttatacattggtgtttgttttc-attagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT-----
                             | | | |  |     | ||||| || |  ||       |  || ||  ||||||| ||| |||||||||||||||||||| || || |     || ||  |  | || ||||||  |||    |||||||| ||||| | |  | | |     
----------------------------gtaagagaaggactaatattttcgatcactcagaaaaaaaaatttgt--gtagATTTTGAGGACATGAGCTGCGAGATGATCTATGGACTCCAGCCGCCCTCTCTCGAAGAGGATCCAGCATTGAAGCAACCATGTCTTG-AACTTTGTAAGTT

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23359 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtaacatatctccttttgaccatccttatacattggtgtttgt-tttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT-----
                          | |    | |||| ||||| | |||| |     ||| | |        |||||||||| ||||||||||||||| |||||||| || ||||     ||  |  |  | || || |||   ||    |||||||| || ||  ||| ||| |     
-------------------------gtacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTCGAAGAAGATCCTGCATTGAAGCAACCATGCCTC-CAGCTATGTAAGTT

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtaacatatctccttttgaccatccttatacattggtgtttgt-tttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT
                          | |    | |||| ||||| | |||| |     ||| | |        |||||||||| ||||||||||||||| |||||||| || ||||     ||  |  |  |||| || |||   ||    |||||||| || ||  ||| |||  
-------------------------gtacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTC-CAGCTAT--

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23185 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtaacatatctccttttgaccatccttatacattggtgtttgttttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCA-GATATAT---
                    | |     || ||   ||  | | |  ||| || |            |||||   |||||||| ||| |||||||||||||||||||| || || |     || ||  |  | || ||||||  |||    |||||||| ||||| | | | | ||    
-------------------gtaagaggactgattttttcatttcttgtttgatcacttgaactctttttttg---tgtagATTTTGAGGACATGAGCTGCGAGATGATCTATGGACTCCAGCCGCCCTCTCTCGAAGAGGATCCAGCATTGAAGCAACCATGTCTTGAACGTTGTAAGTT

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|125063374|gb|EL131377.1|EL131377
EST:     CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTC
genomic: CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTC
EST: gi|124975226|gb|EL048736.1|EL048736
EST:     AATGAGTTTGGCCTCCCACTCACCATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
genomic: AATGAGTTTGGCCTCCCACTCACCATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
EST: gi|124910911|gb|EH984991.1|EH984991
EST:     CCAATGAGTTTGGCCTCCCACTCACCATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
genomic: CCAATGAGTTTGGCCTCCCACTCACCATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
EST: gi|86083117|gb|DR378876.1|DR378876
EST:     CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
genomic: CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
EST: gi|124857037|gb|EH941474.1|EH941474
EST:     CATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
genomic: CATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCT
EST: gi|125165981|gb|EL191995.1|EL191995
EST:     CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAA                         ATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAG
genomic: CCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATGAACCCAAgtatgtaaca ... tggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttatacattggtgtttgttttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT
                               ccatctctccatttt  CT-rich tract
                     ttttcatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaacatatctccttttgaccatccttatacattggtgtttgttttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT