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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT

Basic information

species Arabidopsis thaliana
transcript AT4G32140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 4
gttagaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
                          ||||    ||  |   ||  |  |      ||   |          |   ||   | |||   |    ||||||||| || |||||||| || || |||||||||  ||||||||||||||| |||||||| ||| | ||| | || |  ||||||  ||||||||||||
-------------------------gttagttctttgcttcctttagttgatctgtcttgattcaactgctaattgtttcaacatt---attttagTGCTTCTAAAAAAGTTTGCTGGAGAGGAAGGAGAAAAGGTTGATGTCCAAAAACTGTTTGGCTACCTCGGACTTTTCAGTCTTGTTCTTCTCTGGTGGCT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 4
gttagaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgat--ggcttgta-cccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
                      |||||       || |  |  |  | ||   | |   ||  ||  |||   ||    ||  |||||||      ||||||| ||||| || |||   || || |||||||||  ||||||||||||||| |||||||| ||  | ||| | ||||| |||||||||||||||||| |
--------------------gtaggttggtttgctttgctttatttgcagtggagctctatgaattcggcccctaattgtttcgatattgttt---cagTGCTGCTTAAAAAATTTTGTGGGGAGGAAGGAGAAAAGGTTGATGTCCAAAAACTGTTTGGTTATCTTGGACTTTTTACCCTTGTTGCTCTCTGGTGGAT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 4
gttagaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgat-attgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
           |||| |    || ||   |  | ||  ||| ||    ||   |     || |||  | ||  | ||||   | |||   |   |||| ||||||||||||||| | ||||||||||||||| |||||||||| |||||||||||||| || || ||||| ||||||||||| || |||||||||||
----------gttaagc----aatgtcctggctgttc-tgtttttatcagataatttagatagat--catgaccacttcaactcattactactgcagTTCTTCTTAAGAAGTTTTCTGGTGAAGAAGGAGAAAGGGTTGATGTGCAAAAGCTGTTTGGGTATATTGGATTGTTTACACTTGTAGCACTCTGGTGGCT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 5
gtta-gaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
|||| | ||||     ||| |   | |||    ||| ||    ||  |   ||| |      |||   ||| | |   ||    |||   |   |||| ||||||||||||||| | ||||||||||||||| |||||||||| |||||||||||||| || || ||||| ||||||||||| ||  | ||||||||
gttaagcaatgtcctgtctattctgtttt----tatcagataatttagatagatca------tgaccacttcttcaactc----attactactgcagTTCTTCTTAAGAAGTTTTCTGGTGAAGAAGGAGAAAGGGTTGATGTGCAAAAGCTGTTTGGGTATATTGGATTGTTTACACTTGTAGCATTGTGGTGGCT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G14010.1 (Glycine max), 3'ss of exon 4
gttaga-aatgattaatctttaaaggtttagagtattagtgtgttggggaggataa-cctcattgatggcttgtacc----cttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT--
|||||| ||||  | | ||||   | || |      | || | |||     |  ||      | || |  |  |  |      | | |  || |   | ||||||||||||| ||  || | ||||||| ||||||| |||||||||| |||||||||||||||||  | ||||| ||||||||||| || || ||||||||  
gttagataatgtcttagcttttt-gtttgatttctcttgttttttgtcattgtcaaataatgtagaagaataatgacggattctttaacgttaatgcctcagtgcttcttaaaaaaatttctggtgaagGAGGAGAACGGGTTGATGTGCAAAAGCTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCTTA

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 3
gttaga-aatgattaatctttaaaggtttagagtattagtgtgttggggaggataa-cctcattgatggcttgtacc----cttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
|||||| ||||  | | ||||   | || |      | || | |||     |  ||      | || |  |  |  |      | | |  || |   | ||||||||||||| ||  || | ||||||| ||||||| |||||||||| |||||||||||||||||  | ||||| ||||||||||| || || ||||||||
gttagataatgtcttagcttttt-gtttgatttctcttgttttttgtcattgtcaaataatgtagaagaataatgacggattctttaacgttaatgcctcagTGCTTCTTAAAAAAATTTCTGGTGAAGGAGGAGAACGGGTTGATGTGCAAAAGCTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 4
gttaga-aatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
|||||| ||||  | | ||||    ||||    | |   | |||  |  |   ||     ||  ||| |   | |  |   | || || |  |||||||||||| || ||  || | ||||||||||||||| | |||||||| |||||| ||||||||||  | ||||| ||||||||||| || || ||||||||
gttagacaatgtcttagcttttt--gtttgttttttgtctttgtcagataatttagaagaat-aatgacagcttctttaacgttaatgcct-cacagTGCTTCTCAAAAAAATTTCTGGTGAAGAAGGAGAACGAGTTGATGTGCAAAAGTTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCT

upper sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
gttagaa--atgattaatctttaaaggtttagagtattagtgtg-ttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
||| |    ||  ||||||||      |||  |  | || |  | ||    |  |||  |||||| ||            |||   ||| |     ||||||||||||| |||||||| ||||| ||||||||| |||||||||| |||||| |||||||||| || |||||||||||||| || || || ||||||||
gttggccttatctttaatctt----attttgaaaaactatttagattacatataatattctcattcat------------tctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT

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|125244095|gb|EL258180.1|EL258180
EST:     GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAG                         TGCTTCTTAAGAAGTTTGCCGGTGAAGAAGG
genomic: GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAGgttagaaatg ... gacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGG
EST: gi|86041664|gb|DR337419.1|DR337419
EST:     GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAG                         TGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAA
genomic: GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAGgttagaaatg ... gacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAA
EST: gi|86041665|gb|DR337420.1|DR337420
EST:     GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAG                         TGCTTCTTAAGAAGTT
genomic: GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAGgttagaaatg ... gacaacacagTGCTTCTTAAGAAGTT
EST: gi|86087839|gb|DR383598.1|DR383598
EST:     GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAG                         TGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAA
genomic: GGGAGATCTTTTTGGGCTTCTCTCTGCGGTCTCTTATGGACTTTTTACAGgttagaaatg ... gacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT
                                         tattgac  putative branch site (score: 2)
                                      tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaaatgattaatctttaaaggtttagagtattagtgtgttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG