Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtttcctcctatcaatcaatcaatctcaattattttgtttgatcttttgttgacttcattgttcttgttgttgcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04910.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 1
gtaatgtttcctcctatcaatcaatcaatctcaattattttgtttgatcttttg---ttgacttcattgttcttgttg--------ttgcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
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gta-tgctactctctctttttctcttcatctctatccttttggttctcctttttccctcagtttcatgattttttttccatgtttcttgcagTACAATGAAATCCTTGGCAAAGGAGCTTCAAAGACAGT
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G37180.1 (Glycine max), 3'ss of exon 1
-------gtaatgtttcctcctatcaatcaatcaatc---tcaattattttgtttgatcttttgttgacttcattgttcttgt---tgttgcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
| | | | || | ||| || || | | ||| | | | | ||| | || || | | ||||||||||||||| | ||||| ||||||||||||||||| ||
gtatactattctctctttctctcttcatctctccttcgggttcttcttttccctcagtttcatcatgatgttgttttttccatgtttcttgcagTACAATGAAATCCTTGGCAAAGGAGCTTCAAAGACAGT
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0020g03380.t01 (Vitis vinifera), 3'ss of exon 1
gtaatgtttcctcctatcaatcaatcaatctcaattattttgtttgatcttttgttgacttcattgttcttgttgtt--gcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
||||| ||| | | || | | | | || ||| || || || | |||||| || || | || ||||||||||||| ||||||| ||||||||||| ||||| ||
gtaat-cttcttgttttccttggctt--tgttgctttgttttcttcattttctattgactgtttttgggctgctattttgcagTACAATGAAATTCTTGGCAAAGGAGCTTCCAAGACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctcaattattttgtttgatcttttgttgacttcattgttcttgttgttgcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
tgttgac putative branch site (score: 3)
ttcttgtt putative PPT
aattattttgtttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtttcctcctatcaatcaatcaatctcaattattttgtttgatcttttgttgacttcattgttcttgttgttgcagTACAATGAAGTTCTTGGTAAAGGAGCTTCAAAGACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT