Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.4 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgta-tttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
| || | || | | | | ||| | | | || | || | | |||| || | | |||| ||||| ||||| || ||||| || || ||||| ||||| || || || || |||||||| ||||||| || ||||||||||| |||||||| ||||| || |
----gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaac---cagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 8
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
| | ||| | || | |||| ||| || | | || | | | || | | |||| ||||| |||||||| || || ||||| || || || || || || |||| ||||| ||||| |||||||||||||| ||||||||||||||||| |
--------------------gtatgacatgttcatttgcacatatgagcattttggacattatgactg---attggttaacttgaattagGTTTGGGATTATCAAACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTCTCTGCTGTATGTTTCCATCCTGAGCTTCCAATAATAATGA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
||| | | || || | ||| || || ||| | | ||| | || |||| |||||| |||||||| ||||| || || || || || || || || || || |||| ||||||||||| ||||||||||| |||||||| || |||||||| |
-----------gtttgtcatatgatgcactgaattgtactcctgtggtcatgcatgcactctgtgatgac--attattggt--caaatcagGTTTGGGACTACCAAACAAAGAGCTGCGTTCAAACACTTGAAGGACATGCACATAATGTTTCTGCTGTATGTTTCCACCCAGAGCTACCTATAATAATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
-------gtatgcttctggttaagcttccaatatctgtgctttgattc---ccctgagaattatgtatttgcag--atcgtt-tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
| | || ||| | |||| || | ||| | | | || | ||| || || || | | | || ||| |||||||||||| |||||||||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || || || ||||| || |
gtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
---------gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgca----gatcgtt-tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
||| ||||| || | |||| |||| ||| || || | ||||| || | || || | | | | || ||| |||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||||| ||||| || || || ||||| || || || ||||| || |
gtttgttttctat-tttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctt----tgattcccctgagaattatgtatttgcagatcgtttactag--tggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| | || | || ||| | | ||||| | | | | | | | | || | | | || | || |||| |||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| || |
gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatgaaaaggaataacatggatgaaacttacgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
-----------gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgcagatcgtt--tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
| || | || | | | | | | | || || | | || ||| ||| || | | | | || |||| | |||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| || |
gttttgttttcatttgttgcttgatctatctgct-tgtacgcatttacatatacatacatatatatatatatgaaaaggaataacatggatgaaacttatgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgca-gatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| ||| || | | || | | ||||| || | | | | || | | | || | || | | | | | ||||| |||||||||||||||||||||||||||||||| || || || |||||||||||||||||||| || || |||||||| || ||||| |||||||| |
gtctgccgttgataattattttca-agctgtgtttagtatttatgcggtttgatagaaggaaatgttcatggacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| | |||| | | | || | |||| ||| || || | || | || | | | | ||||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||||||||||||| | || |||||||||||||||||||| || || | |
gtgtttatctgat-gcttattgactaaata-gcttccatttatgtgcattccatttgattactttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTAMapped 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|116382436|gb|EG425028.1|EG425028EST: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAG GTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
genomic: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAGgtatgcttct ... actttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
EST:
gi|116382434|gb|EG425026.1|EG425026EST: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAG GTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
genomic: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAGgtatgcttct ... actttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
ctttgat putative branch site (score: 5)
tactttttc putative PPT
agaattatgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT