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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G24620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g37380.1 (Oryza sativa), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgt-tgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                                              |   | | ||    ||||  | |   |   | |||||      | |||  ||| ||| |||  | |||  |||  |||    |  |||   ||| ||| | ||||||||||| || ||||||||||| || ||||||||||| |||||||||||||| || || ||||| || || || ||| | ||  |||| || ||||||
--------------------------------------------------------------------------------------------gctcgtttgcaatgtaatgtattgttaaaatgtcttctgcagctcaaagt--actgtgtgtgtgaagtgtgatctacctt---atctttctgatggctgt-gtcagATAAGATTTATCGACAACACCGATCCAGCTGGAATTGACCATCAGATTGCACAGCTAGGACCAGAACTTGCATCAACTCTTGTGATTGTAATATCAAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g29070.1 (Oryza sativa), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                             |  ||| |||   | ||   ||   | |   |    ||| |       || ||  |  ||| ||||           | || |    ||| |    || |   || || || ||||||   |||| |   |  |||||| |||| ||||||||||| || ||||||||||| || ||||| ||||| ||||| || |||||||| || || ||| | ||| |||| || || |||
----------------------------------------------------------gtgcgcccctacttttatatccatgcaatgtgcttcgatctcatt------tgcccctttgtagatttt----------ggtgtttctcatgtag----ctataacctcaccttttgttctg--tttgatgtct--cagATACGATTTATTGACAACACTGATCCTGCTGGAATCGACCATCAAATTGCTCAACTAGGACCAGAGCTTGCATCTACTCTTGTAATTGTTATTTCTAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G140614_T02 (Zea mays), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttg-ttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                         |   |  ||   |   ||| | ||   | | ||  |   | | | |   | |||| || ||||       |   ||||    | ||    | | ||  ||    | |  | || ||  ||   |||||||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| || || || |||||  | ||| | ||| ||||||| || |||
--------------------------------------------------------------------gtatgcccctaagt---cagaatcctagcaatgcacaaaaaatgcatttgtctagcttttgtgtttaa-------tgtcttgtcagtt-ctaagatataaccctaaacccgtattatgcttaatttctagATAAGATTTATTGACAACACCGATCCTGCTGGGATTGATCATCAAATTGCTCAACTAGGACCTGAACTGGCAACTACTCTTGTAATTGTCATTTCTAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G076075_T01 (Zea mays), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttg-ttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                              || ||| |    || |  |        |||   ||   | |  |  ||  | | | |     |||| | ||||| |    ||  |  ||||     |||      |   ||   ||||  | || ||| ||   |||||||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| || || || |||||  | ||| | ||| ||||||| || |||
------------------------------------------------------------gtatgcccgcccctaagtcaga-------atccgagcaatgcatgaaaattacatttgtctatcttttgt-attaagatgtcctg-tcagttgcaagatgt-----aagcctaaactcttgttatgcttgatttctagATAAGATTTATTGACAACACCGATCCTGCTGGGATTGATCATCAAATTGCTCAACTAGGACCTGAACTGGCAACTACTCTTGTAATTGTCATTTCTAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G09800.1 (Glycine max), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                                              |    | |   |   || ||    || |||   |    |||    | |   |       | || || |    |||||| | ||||| |  |  |     ||||||||||||  | |||||||| || |||||||||||||||||||||||||||||||||||||| ||||| || || ||  | ||  |||| || ||||||
--------------------------------------------------------------------------------------------agtaatccatgggaatttgcccctaatt-ggtgaattcagttatttcatttctcacaaggatttagtgat----gactttgtcttctttcacttctctaccacagATAAGATTTGTGGACAACACGGATCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCTGAGCTAGCTTCAACACTTGTGATTGTGATATCAAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G37590.1 (Glycine max), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttct----gattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                                                       |||  |   | |   ||| ||| ||      |||  ||  || | |  |  ||    | |||| |  |     |  |   |  ||||  | ||| ||||||||||| ||||||||||| || ||||||||||||||||| |||||||| |||||||| || ||||| || || ||  | ||  | || || || |||
---------------------------------------------------------------------------------------------------aaccaaacaacccctttagttatgttctttgaggagatctaataaggcaatatc-ttacacattgttatggggtaaaacatatgtt-tttgacttttggcagATAAGATTTATTGACAACACGGATCCTGCTGGAATTGATCACCAGATTGCGCAACTTGGTCCTGAGCTAGCTTCCACACTTGTGATCGTAATTTCGAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G09880.1 (Glycine max), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                                              |    | |   |   |  |  ||| |  |||  |    |||      |   |       | || || |    ||||||   ||||||  ||   |    ||||||||||||  | |||||||| || ||||||||||||||||||||||||||||| |||||| | ||||| || || ||  | ||  |||| || ||||||
--------------------------------------------------------------------------------------------agtaatgcatgggaaatttgctcctcatttgttaattcagttatttcgtttctcacaaggatttaatgat----gactttgccttcttcacttctctacc-acagATAAGATTTGTGGACAACACGGATCCTGCTGGAATTGATCATCAGATTGCACAGCTTGGGTCGGAGCTAGCTTCAACACTTGTGATTGTGATTTCAAAG

upper sequence: AT4G24620.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g07280.t01 (Vitis vinifera), 3'ss of exon 2
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                                                                                   | |||| | | ||   |    || | |      || ||  | || ||  ||    |  ||| |||||         | | ||  |  || | || ||  |||||       ||||||||||||||||| || || || || |||||||||||||| |||||||| || ||||| || ||||||||||| ||  ||||| ||||||| ||||||
-----------------------------------------------------------------------------gaaaaatcctttctatctggtgctatgaaagctaattgatcgtatttcttcctattt----ggatctcctttg---------gatgtcaaaaattttattgttattttgg-------cagATAAGATTCATTGATAATACAGATCCAGCTGGAATTGATCACCAGATTGCCCAGCTTGGCCCCGAGCTGGCCTCTACAATAGTAATTGTCATTTCAAAG

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|47831857|gb|CK121541.1|CK121541
EST:     GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
genomic: GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
EST: gi|116478091|gb|EG520683.1|EG520683
EST:     GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCC
genomic: GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCC
EST: gi|116436183|gb|EG478775.1|EG478775
EST:     GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
genomic: GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
EST: gi|125032807|gb|EL105076.1|EL105076
EST:     CCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
genomic: CCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
EST: gi|116436172|gb|EG478764.1|EG478764
EST:     GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
genomic: GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
EST: gi|47831767|gb|CK121451.1|CK121451
EST:     GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
genomic: GACCTCAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCA
EST: gi|124765848|gb|EH855978.1|EH855978
EST:     CAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAG                         ATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGAT
genomic: CAATTTGTCGCTGAGGCCTTGGCTCCTGATAATCCTCCATTGAAGgtatcgcata ... ttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG
                    ttctgac  putative branch site (score: 2)
                                 ttcttcctttggtt  putative PPT
                           tttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgcatactgttctaattgcagtcaacattacattcccttgctcttaacactcttagccatccccactaacaaatgggtgttctttatctttgcctcgtaaaaggatgtcctctcttaggtttttctgattaaaagagtctactttgttgtctactgttttctgactttatgttcttcctttggttgttgacagATAAGATTCATTGACAACACCGACCCTGCTGGAATTGATCATCAGATTGCACAACTTGGGCCAGAGCTGGCCTCGACTTTAGTAGTTGTCATCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT