Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G38510.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------gtgagctgcttta-----gcctcttgtcacataattactatctcataataaaacacacagata-taattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                                                   |   | |  ||||      |   | ||  |  || |  ||| ||       |  | |   ||| |   |   ||  ||| ||   ||||||||||| || ||||||||||| ||||||||||| ||||||||||| || || || ||||| |||||||||||||||||||| || ||  |||| || ||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttatt---ccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------gtgagctgctttagcc-tcttgtcacataattactatctcataataaaacacac----aga---tataattctagacttttgtttc--tccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                                                                 ||     | |||||   | |||    || |     ||   || |   |   ||     | |   | ||||  |  ||| |  |||   | ||||||||||||| ||||||||||||||||||||||| || |||||||| || || || ||||||||||||||||| |||||||| || ||  | || || ||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttttgttt--ctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                                                                           | ||  |  || |    |||    | |   |  |   |||  | |||        | ||| | |  ||| |  |||  || ||||||||||||| || |||||||||||||||||||| || |||||||| || || || ||||||||||||||||||||||| || || ||  | ||||| ||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattt-----tgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagactttt----gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
      |  || |    |||  ||      ||| ||   ||  | |          | |    |   |  | |      |  | |||||||||| |||||||| |||||||||||||||||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || ||
-----gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
       |  | |   |  |       |  ||  |     ||     |        | |  |  || |       |  | |||||||||| ||||| || |||||||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||| || ||||| || ||
-------gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 6
gtgagctgctttagcctcttgtcacataattactatct-cataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA-
         | ||   |||| |       |    || | |||  |        |   | ||| | |   |  |   |  | |||||||||| ||||| || ||||||||||||||||| || |||||||| ||||| || ||||| ||||||||||||||||| ||||| || ||||| || || 
-------tatataatttcttctggggaggtctgaatatgcatgtttttctttgcctttttaaatattttccctg--taattcaggAAGTTCCATCAACCCTAGTGAGAGAACCTATCCAGAGGAGATGATACAGACAGGAATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAAG

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagactttt----gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
      |  || |    |||  ||      ||| ||   ||  | |       |  | ||   |   |  | |      |    |||||||||| |||||||| |||||| ||||||| ||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || ||
-----gtatttaacttcctttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtgagctgctttagcctcttg---tcacataattactatctcata-ataaaacacacagat---ataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                |||   |  |||| ||  |     |||| |    ||| |    |  | || |    |||||    || |  |   ||||  ||| | |||| ||||| |||||||| ||||||||||| ||||||||||||||||| ||||| || || || || |||||||||||||| ||||| ||||||||||||||
gtgagttttttaggaggtggtattatttaaccattaaaactcacctctgaactttagagtttacaacagtggcagatcctgtactctttttctttccttttttcagGGAGTTCCATCAATCCTAGTGAGAGAACATATCCTGAAGAGATGATCCAGACAGGGATTTCTACAATTGATGTCATGAATTCTATTGCCAGAGGACAGAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------gtgagctgctttagcctcttgtcacataat-tactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                                  || |   |||  |   | |||  | ||  | | ||||    |  || |      | | |   | || ||    |||  || ||||   ||| ||||| || |||||| | || || ||||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||  |||| || ||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttga----tgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttt-tgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                ||    | |  || ||||          | || | | | |  ||  || | |      || |  |  | ||    |  |  ||||   ||| |||||||| |||||  | || |||||||| |||||||||||||| || ||||| || ||||||||||||||||| ||||| |||||||| ||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------gtgagctgct--ttagcctcttg-tcacataattactatctcataataaaacacacagatataattctagacttttgtttctc-cagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                          || ||  |||||| |  | ||    ||          ||  | ||  | | |  | ||||  || | |     |  || ||||    || |||||||| |||||| | || || || || ||||||||||| || || ||||| || |||||||||||||||||||| ||  |||| || ||
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

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|86066802|gb|DR362559.1|DR362559
EST:     CATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
genomic: CATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTGgtgagctgct ... gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
EST: gi|86066806|gb|DR362563.1|DR362563
EST:     CATTGACAACGGTCCACCTATATTGCCTGAGGCGNACTAGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAANAGATGATTCAGA
genomic: CATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTGgtgagctgct ... gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     GGCGTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
genomic: GGCGTACTTGGATATTTCTGgtgagctgct ... gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
EST: gi|86066801|gb|DR362558.1|DR362558
EST:     CATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA
genomic: CATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTGgtgagctgct ... gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA
                                        cttttgtttctcc  CT-rich tract
     tatctcataataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA