Sequence
atgc intronic sequence ATGC exonic sequencegtatctacagaatagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57690.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G073380_T01 (Zea mays), 3'ss of exon 3
gtatctacagaatagaaacaaga-acacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgt---gtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
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-------aagctcacaatttctctgttttttttggatagcgtacgtagggatcatccttccgcatatagagcgtgaaattaatttcatctgacactctatgatgcagTGTGAGGGCAATCGTTGCATTAAATCTTCACAATTATGCAAGTGGAAGAAACCCTTGGGGAAATTTGAAGCCTGAATATTTGGAGAAA
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
gtatctacagaa--tagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
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ctgcctagagaatttagcaagagtcacacaactcaatct---cttttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttccttt--cagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 9
--gtatctacagaatagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
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tactgcctagtgaatgtagtaagagtcacaactcagtct---ctttcgtgaagtttttggtttggtccattttgcatgatatggttatgttatttccttt--cagTGTAAGGGCAATAGTTGCTTTGAACCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGATTATTTGGAAAAG
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
gtatctacagaatagaaacaaga-acacaaatgagacagaac--actttta-aatctcataattgggtt-tctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
|| | | | | ||| | || || | || | ||| |||||| | || || ||| || | || | | || || || ||||||||||||| | ||||| | ||||| ||||| ||||||||||||||||| || ||||| ||| | | || || ||| | || ||
------tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgtttt--cagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
gtatctacagaatagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgt-gtttgcttgtttttgggac----agTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
|| ||||| ||| | | | | || | | | || | | | | || | | | || | || || || ||||| || ||| | ||||| |||||||| ||||||||||||||||||||| | || ||||| ||||| || | ||| ||| | |||||
-------caaaatagcaacctttttttattttttatttctttttcttga-tttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
ttctaat putative branch site (score: 2)
cttgttttt putative PPT
tttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctacagaatagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA