Sequence
atgc intronic sequence ATGC exonic sequencegtaataatctcacgatttgcttcttctaaagtaattaaatggatcactgtggaatctggacttaaataaagtactgatattggtatcattttggttgcaacttgtttgataatgtgatgatatctcatatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65410.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------gtaataatctcacgatttgcttcttctaaagtaattaaatggatcactgtggaatctggact--taaataaagtactgatattggtatcattttggttgcaacttgtt--tgataatgtgatgatatctca--tatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG---
||| ||| | | | || | ||| | | | | | | || | | | | | ||| | ||| | | |||| ||| || || | | | ||| ||| | | || || |||| || | | | || | | | | | | | |||| |||||||||||||||||||||| ||||||||||| ||||| || |||||||
gtctataatttgatttcattcctattgttgcattgcaagttccttctttttttttattcaatgatcacgtgttgtg-tccttttttgttgttggggttggtgttgagtgagtttagctttctgggtaatcagaaagttttgtttttttttttgttttcctttcttccttctgggtggctgacatcaaggttgttgctagGGTTCGTCCAAATCAGAACAAC---TGAGCACGGCGTGGGATCATGAGGATGATTCTGATGTTCTTATTGAGTGTAGAGATGTGTATAAGTCTTTTGGGGAAA
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 1
-------------------------------------gtaataatctcacgatttgcttcttctaaagtaattaaatggatc-------actgtggaatctggacttaaataa------agtactga-tattggtatcattttggttgcaacttgtttgata-atgtga-tgatatctca--tatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG--
| || || ||| | |||| | | | || || ||| | ||| |||| | | | | ||| || | | ||||| || || || | ||| ||| ||| | | || || |||| || | | || | | | ||| | | |||| |||||||||||||||||||||| |||||||| || || || || |||||||
tgtaaatgtctttaatttgattcattcctgttgttgcattgcaagttccttcttttttgcttcaatgatcacgtgttgtgtccttttctgttgttggggttggtgttaagtgagttcggattcctgggtaatcagaaagttttgtttttgtttttcttcttctgggtggctgacatcaaggttgttgctaGGGTTCGTCCAAATCAGAGCAAT---TGAGCACTGCGCGGGATCATGAGGATGATTCTGATGTTCTTATTGAGTGTAGAGACGTGTACAAGTCTTTTGGGGAA
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 1
---gtaataatctcacgatttgcttcttctaaagtaatt--aaatggatcactgtgg--aatctggacttaaataaagtactgatattggtatcattttggttgcaacttgtt-tgataatgtgatgatat---ctcatatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG---
| | ||| || |||| | | | || | |||| | || ||| | | || | | || ||| | | |||| ||| | | ||| ||| | || | || | | | | | ||| || | | |||| || ||| | |||| ||||||||||||||||| |||| ||||||||||| ||||| || |||||||
gtaaaatcattcttgtttttggcttttcgtttttttgttttatatggttttctttggttagctcgttttttttttttccattgg-attctttttgtttt--ttgaagaataccatgaatttgttctcatttgggttctctcttattagGATTCATCTCATCTAAAGAATCCAAGTGTT--GATGGAGACCGTGAGGATGATTCTGATGTTCTTGTTGAGTGTAGAGATGTGTATAAGTCATTTGGGGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtatcattttggttgcaacttgtttgataatgtgatgatatctcatatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG
gtttgat putative branch site (score: 5)
tttgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataatctcacgatttgcttcttctaaagtaattaaatggatcactgtggaatctggacttaaataaagtactgatattggtatcattttggttgcaacttgtttgataatgtgatgatatctcatatctgcagAGTCTTACCAAGTCTGGAGGAGGTATGTGTAAAGAGCGAGGGCTTGAGAATGATTCTGATGTTCTTATTGAATGTAGAGATGTCTATAAATCGTTTGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG