Sequence
atgc intronic sequence ATGC exonic sequencegtaattttcctggttttggacaatgtgcttagtttgtatgtcgtttgattcttggttattaaattgtgttttttcttttttcttgtagAGGATCACCACTTTTCTGGATTGGTGTTGGTGTTGGTCTATCAGCTTTGTTCTCATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtaattttcctggttttggacaatgtgcttagtttgtatgtcgtttgattcttggtt---attaaattgtgttttttcttttttcttgtagAGGATCACCACTTTTCTGGATTGGTGTTGGTGTTGGTCTATCAGCTTTGTTCTCATAT
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gtaatcatttactcttttttttctttggcatattaattttcttaaaaaaaaattgtcatatttttataatgggtaactactaactactgggggtgggggtggttgatcgatactttattgatttaaatttgttg-atatctattgcttattagttcacattcttattggtcctatttactatattctagAGGGTCACCTCTCTTCTGGATTGGTGTTGGTGTTGGGCTTTCTGCACTGTTTTCAGTG
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 2
---gtaattttcctggttttggacaatgtgcttagt-ttgtatgtcgtttgattcttggttattaaattgtgttttttcttttttcttgtagAGGATCACCACTTTTCTGGATTGGTGTTGGTGTTGGTCTATCAGCTTTGTTCTCATAT
|||||| | |||| || | || || | | || || ||| |||||| ||| || | || | | || ||||| ||||| || ||||||||||||||||||||||| || || || |||| |||
gtaataatttactcttttttatttaaatttgttggtatcctttgctcattagttcaca-ttatta--ttg-gtctatttactatatttccagAGGGTCACCTCTCTTCTGGATTGGTGTTGGTGTTGGGCTTTCTGCACTGTTTTCAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatgtcgtttgattcttggttattaaattgtgttttttcttttttcttgtagAGGATCACCACTTTTCTGGATTGGTGTTGGTGTTGGTCTATCAGCTTTGTTCTCATAT
gtttgat putative branch site (score: 5)
ttgtgttttttctttt putative PPT
ttattaaattgtgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttcctggttttggacaatgtgcttagtttgtatgtcgtttgattcttggttattaaattgtgttttttcttttttcttgtagAGGATCACCACTTTTCTGGATTGGTGTTGGTGTTGGTCTATCAGCTTTGTTCTCATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT