Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgtcgtttcatgttaagagctaatcttaatgttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgtagGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g25460.1 (Oryza sativa), 3'ss of exon 2
----gtatgttgtcgtttca--tgttaaga-gctaatcttaatgttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgt-agGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
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acagaaatttttacattatagctgttagtctgttgaaataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
upper sequence: AT3G24210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G140394_T03 (Zea mays), 3'ss of exon 2
--gtatgttgtcgtttca------tgttaagagctaatcttaatgttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgtagGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
| |||| | || | | || || | | | || | | | | | | | || | || | ||| |||| ||||||||||| || |||||||| | ||||||||| ||||||||||| |||||||| | |||| |||||||||| | || || | ||| || |
ttgctctttgttgattaaacaatttcttccctgcaagttatgatcctttcggtgccattgtaatagtgaattatagctcagtaaagattttccctcccagGTCGCTATTCCAGTCGTGCCTACAATCAGAGTGCTTGTGACATTCACAAAATTTGAAGAGCTACAGCCGCTAGATGAGTTCACCACACCACCCTCAAGTC
upper sequence: AT3G24210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0136g00240.t01 (Vitis vinifera), 3'ss of exon 2
---gtatgttgtcgtttcatgttaagagctaatcttaatgtt--cttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgta----gGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
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tttacctgtgattattatttcttccaagcagcttcttgggttggctgttgtatttctgtatttgtctatttgcta-agaagtcctctatagttatatccagGTTGCAATTCCTGTGGTTCCTACCATCAGAGTGTTGGTTACATTTACAAAGTTTGAAGAACTACAGCCGGTGGATGAGTTTACAACACCCCCTTCAAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgtagGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
tttttttttctttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgtcgtttcatgttaagagctaatcttaatgttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgtagGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA