Sequence
atgc intronic sequence ATGC exonic sequencegttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtc-atgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| | | || | || | | | | ||||| ||| | || | |||||||||||||| |||||||||||||| |||||| ||||||| ||||||||| || | ||||||||||| || || ||||| ||||||||| |||
-------------------------------------------------------------gtaacttattatctttgttctttatcaggttatccttagatgcaccattcttaatttatgtttgt--agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcat--gcattgttcattccctacatcaa-acaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
|| |||| || | | | | ||| ||| | | |||| || | || | | | || | |||| | | |||| | |||||||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||| || |||||||| || | ||| || ||||||||| |||
-------------------gtaaaatttaaagtcacttgtgcctga--aaattatatggagctgcatggaatttctcttttgttttctatttcattggtgttaacatttccagtgcatcttatcattgccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgt-catgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| || | || | ||| | | ||| || || | ||||| |||| || || || |||| || ||||| || ||||||||||| ||||||||||| ||| | ||||| || |||||| || | || ||||||||||| | | || |||||||| |||
-----------------------------------------gtaagcaggccttttgaattttctatta---------gcctctg--gatttcactgttcatgttttatt--tttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
|| ||||| || || || || | | | || || ||||||| | | ||| | || ||||||||||||| |||||||||||||| || ||| ||||||||||||||||| | | ||||| |||||||| |||||||| ||||| ||| |||
----------------------------------------gtcagccaaaattagctatgtt--catctgagcgtccttagatgtatgta-tgactgttgatttaccctaaggtcctctgtttggca-gGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| |||| || || ||| ||| || | || | ||||| | | | | | || ||||||||||||| |||||||||||||| || ||| ||||||||||||||||| | | || || ||||| || |||||||| ||||||||| |||
----------------------------------------gtgagctaaaattagctat-cttgaacctaacgttctta--gatgtatgtattactgttgatttacactaagatcatctgtttgcca-gGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 5
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| |||| || || || | || | | | | | || | || | | || || | | |||||||||||||| |||||||||||||| || ||| ||||||||||||||||| | | || | ||||| || ||||||| ||||||||| |||
----------------------------------------gtgagctaaaattagctatcttgaacctaacgttcttagatgtatgtattactattgatttacactatg-atcatctgttt---gccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAATATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 1
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| |||| || || || | || | | | | | || | || | | || || | | |||||||||||||| |||||||||||||| || ||| ||||||||||||||||| | | || || ||||| || ||||||| ||||||||| |||
----------------------------------------gtgagctaaaattagctatcttgaacctaacgttcttagatgtatgtattactattgatttacactatg-atcatctgttt---gccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaat--aaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
| || |||| | | | || | || | | |||| | ||||| || ||| | | |||| || | | | || || | || ||| || |||||||||||||||||||||||||| |||||||||||||||||||| |||||| |||| || || ||||| |||| ||||| ||||||||||| |
------gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatg----------gttgtgactga-ctaatttttattaatgaa--actcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 7
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacattt-gcac----caaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
||| | | | || | ||| | || | | ||| | | | | || |||| | ||| | | | | | | | | | | | | || || | |||| ||||||||||||||||||||||||| ||||| |||||||| |||||||| |||||||| || || |||||||| |||| ||||| ||||||||| | |
----gtgagtactattaataattcca--tgtttcactttctcagaatcatcctgtctctcttgagcactttcctcaaagtggcttcttcattctgttaattattgt----catcttttttcttcctcaaccaagGTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
agctgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA