Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 5
gtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT---
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---------------------------------------------------tagtttaatgtgactgtaaactgccttgatcagttttaagtagaaaa-caacatata---tcctttgtccctctcccatcacaagttcttgtta--tctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTATACCTGTCAAGAAAG---GCTGGTTCAGCATCACCAGTTAGTGGATCAG
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
gtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT---
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---------------------------------------------------aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaa-caacatatatccattttccctctcccatcacaagttcttgttatc-----tggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAG---GCTGGTTCAGCATCACCAGTTAGTGGATCAG
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT
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---------------------------------------------------acattttccatcagca-gcagttgat---caattatctgctcaatttgtatgcttcacagcctt--aacactaaagacttcatatggtgctcataactgattgcagGTGAGGGATGAGCTTGAACAACTTCTGGATGATGATGATGATATGGCTGATCTTTATCTGTCCAGAAAATTGGCTGGTGCATCTTCACCAGTTAGCGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT
aattaat putative branch site (score: 3)
tctctctcgtcgcttt CT-rich tract
aagaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA