Sequence
atgc intronic sequence ATGC exonic sequence...attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggatatatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G337631_T01 (Zea mays), 3'ss of exon 6
attgtagagaagtcgaagtataactcaaa-aggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggatatatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
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-ttgagttgcagccaaatctcgccccaactaactttttttcctgggtccgccactgataactgtatacattcttgtggcggtgatccttaattgatggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTATGACACTGCTGGACCCTGCTACTAGAGGTCGAATGCTACCATCACCG
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G074664_T01 (Zea mays), 3'ss of exon 4
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggatatatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
|| | || || || ||| | | | | | | | || | || | | || ||||| ||||| |||| |||||||| ||||| | |||||||||||||||||| | | | || ||||| ||||||| || || | || || ||
tttaagttgcagctaaatctcgctccagctaactttttttctaggtctgccactgataaatgtatacattcttgtggcggtgatccttaattgatggcagGTGGAAGAAGAGACCGGTATAAAGCTGAATATAGAAGATATGGTTGATCTTATGACACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 5
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggata-tatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT-
|| | || || | || ||| | | | | | | | || | || | | | | | | | | ||||| ||||| |||| ||||||||| ||||| | |||||| ||||||||||| || || | || ||||| ||||||| || || | || || ||
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggt-gatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGG
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 4
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggata-tatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
|| | || || | || ||| | | | | | | | || | || | | | | | | | | ||||| ||||| |||| ||||||||| ||||| | |||||| ||||||||||| || || | || ||||| ||||||| || || | || || ||
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggt-gatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggatatatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
atatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggatatatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
- - - - - - - - - - - actcaaa
- - - - - - - - - - - - - - - - - - - acaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg