Sequence
atgc intronic sequence ATGC exonic sequence...ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttgtgcctcatgtttttttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G08380.1 (Glycine max), 3'ss of exon 1
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttg--tgcctcatgtttttttttttttttttggcc-attgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
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---ctactaatgcagtgaaaatgctgtctggattcagtgatatttattcactatatagattaagctaactgtagctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G44450.1 (Glycine max), 3'ss of exon 1
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttgtgcctcatgtttttt----tttttttttttgg--ccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
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-----ctaccaatgcagtgaaaatgctgtttgtat-ttagtgatatttattcgttatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttg--tgcctcatgtttttttttttttttttggcc-attgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
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---ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G47100.1 (Glycine max), 3'ss of exon 1
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtctt---ttgctttgtgcctcatgtttttttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
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--atctccagcaattgtat-gtgttaaagagttaattgaatatctggtgaaaatgtcgtttcatcttacattgtgttggacttatgggttctctctttactagACTCGGTTAACGATATGTGAGGGTCATGATGGGACTGAGACATCTAATGGGGATGTGTTGATCTTTCCTGACATGGTTAGATACAG
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G01640.1 (Glycine max), 3'ss of exon 1
-----ggattgcttcttttcgga--tagtctcatgatgatgccttcatgattgtcttttgctttgtgcctcatgtttttttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
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ttcatcaaatgtatgtgttaagagttagttaattgaatatctggtgaaaatg-----ttgcttcgt--cttacattgtgttggacttatgagttctctctttactagACTCGGTTAACGATATGTGAGGGTCATGATGGGACTGAGACATCTAATGGGGATGTGTTGATCTTTCCTGACATGGTTAGATACAG
upper sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0015g00750.t01 (Vitis vinifera), 3'ss of exon 1
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttgtgcctcatgtttt--tttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
||| | | | | ||| | | || | | | | | | || | | | ||| | | |||| |||| || || |||| || | ||||||||||| || ||||||||||| |||||||| ||||| |||||| | || ||||| || ||||||||||||||
--attcatgaatattgccagatctgcagtttatttttccttcctgttgtagtgactgagggttaatggtatgattttgccgttttctatttttcttctcaagACCCGCTTAACAATATGTGAAGGACATGATGGAACTGAGACATCAAATGGAGATGTATTAATATTTCCAGACATGATCAGATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttttgctttgtgcctcatgtttttttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
tttttttttttttttt CT-rich tract
tcatgttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttgtgcctcatgtttttttttttttttttggccattgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
- -ttgcttc