Sequence
atgc intronic sequence ATGC exonic sequencegtacagtaaaatattcttgtgtacttggttcgaacttaacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G45332.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 10
----------------------gtacagtaaaatattcttgt-gtacttggttcgaacttaacataatttgcttctc----tagggatgaaagtctgatattgtgtttcttgttgg----gtcactt-ttcctaaatca---gGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
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gtaaatttttgagtgaagtgtagggccacaggctattcaagaagtacctctgtccactatactaccatgtgctcttcgattttctgttgacattttcggatt-tgttctgtgttggtctgattatttgttctcgcatcaatagGTGATACATTTACAGATGGATCAGTGAAATATACCATGACTTCCATGAATGTCCCTGAACCTGTGATGTCCTTGGCTGTCTCCCCTATATCTAAAGATTC
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 10
gtacagtaaaatattcttgtgtacttggtt-cgaacttaacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
|| | || || | | |||| || ||| ||| | | | || || | | || || || | ||| ||| |||||||||||||||||| |||| || || || ||||| || ||||| || ||||||||||| |||||||| || ||| ||| | || ||||| ||
----------gtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcattt--attctggatctgacttttcacttctctttgtcaat-agGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 10
gtacagtaaaatattcttgtgt-acttggttcgaacttaacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
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---tgatgcttcattccaattttgcttatattgctctttgcttcatttgtttc---atatatatatatat-atatttcatgatatctaaacttctttttgtca--tcagGTGATACTTTTACTGATGGGTCAGTGAGATACACCATGACCTCTATGAATGTTCCAGAACCGGTCATGTCATTAGCTATTTCACCCGTTTCTAAGGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
tcctaaa putative branch site (score: 2)
tcacttttcct CT-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtaaaatattcttgtgtacttggttcgaacttaacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT