Sequence
atgc intronic sequence ATGC exonic sequencegtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22770.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 9
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
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----------------------------------------gtaagctcttatgatcctgtccactgttgtaccatgtgtactttccaaat---gattgctaacatgctatttt------tcgtcagATACTATGCAATTGCTACTCCAAGTGCTACCCAAAGGTTGCTTTTTGGTCTTCTCGAGGCACCACCATCATGGGCCCCAGATGCACTTGATGCAGCAGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 9
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
| || | | |||| ||||| | ||| || |||| | | | | || | || ||||||||||||| ||||| || ||||||||||| ||||| | ||| |||| || | ||||||||||| || ||||||||||||||||||||||| || |||
-----------------------------------------------------gtaagctccagttcactgctatgcttaatcc--acttcaagat-atttttttagtgggatcttttcctttcagATACTATGCAATTGCTACACCAAGTGCTACACAGAGGTTGCTTTTTGGTCTTCTGGAAGCACCACCATCATGGGCTCCAGATGCACTTGATGCAGCAGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 8
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
||| ||| | |||| | | | ||||| | | | |||| | | || | | | | || | | |||||| ||||| ||||| || ||||||||||| ||||| | ||| |||| || | |||||||| || || ||||||||||||||||||||||| || |||
-------------------------------------------gtaatct----ccagttc-actgctatgctttcatctacttccagataaaa------ttttaaatgggttatttt-ttcccagATATTATGCAATTGCTACACCAAGTGCTACACAGAGGTTGCTTTTTGGTCTTCTCGAAGCACCTCCATCATGGGCTCCAGATGCACTTGATGCAGCAGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
| | | ||| || | || || ||||| ||||| || | || | | | | || | | | | | | | | | |||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| | |||||||| || ||||||||||||||||||||||||||||||||
-------------------------------gttattttgaacttaatacctttcttgttttttagttgt---tcatagagttcatctgcctgacaaaatat---atatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 8
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttg-ctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
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-------------------------------gttattttgaacttaataccttatcttgttttttagttgt---tcatagagttcatctgcctgagaaaatat---atatacacctaacctttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTAGAAGCACCCCCATCATGGGCTCCAGATGCACTTGACGCTGCTGTG
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 8
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
| | | || | | || |||||| | ||||| |||| ||| | | | | || ||| | | | |||| ||||| ||||||||||| ||||| ||||| || || ||||| ||||||||||| ||||||||||| || || |||||||| ||||| ||||||||||||||
-------------------------------gttattctgaactcaatacctttctagttattttgttgt---tccttcaatgcattggcctgagcaaatttat-atatctaaattat----ctagATATTATGCCATTGCGACTCCTAGTGCAACTCAAAGACTACTTCTTGGACTTTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTG
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 9
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactt-tcctgttatactgtc-agATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
|| || | ||| | || | | | ||||| | | | | | | || | | | | || ||| | ||| || ||| | | | ||||| || || |||||||| ||||| ||||||||||| || || |||||||||| ||||| | ||||||||||| || |||||||||||||| ||||||||||| |||
gtgaatttccatacctttctctgtgggtaactttttatggaaaacatttcctaatttattctttcttccttttatcttttttccttttatcttttttccttttttggtggtggggttatctggtttagCTACTATGCAATTGCTACTCCAAGTGCCACACAACGACTTCTTCTAGGACTACTGGAAGCACCACCATCATGGGCTCCAGATGCTCTTGATGCTGCAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
ttctcac putative branch site (score: 2)
aattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT