Sequence
atgc intronic sequence ATGC exonic sequencegtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtctaacaatattttttttctattaaaatatgtctaatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20820.1 (Glycine max), 3'ss of exon 2
gtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtctaacaatattttttttctattaaaatatgtctaatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
| | | || ||| |||| || | ||||| | | | | | ||||| || |||| || | ||||| || || | | |||| || | | |||| | ||| |||||||||| | ||||| ||||| |||||||||||||||||||| |||||||| | | || | ||||| || ||| |||||| ||||| ||| | |||
--------gtatgtaacgatgcttctc---ttttccttaca----caaaattctgtttctgttc---tttttttattttattttaaca-atctaa-attggagaggaa-----atttatggt--ggcatttgtgtgtt-----tcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCATTCTGAAGCACTTGGGAATAAGGGAATACTTCTCGGAGATTAACACTAAC
upper sequence: AT1G73010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01410.1 (Glycine max), 3'ss of exon 2
gtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtctaacaatattttttttctattaaaatatgtctaatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
||| || | | ||| ||| ||| | || | | | | ||||||| || | | || |||| || | | |||| | |||||||||||| | ||||| ||||| |||||||||||||||||||| ||||| || | | || | ||||| || ||| || || ||||||| | |||
------------------------------------------gtatgtaactatgcatttcttacacaaaattctgttttgtgaaatatg----atttggggtggaa------atttatggt--ggcatttgtg-------tttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACTATTCTGAAGCACTTGGGAATAAGAGAATATTTTTCGGAGATCAGTACTAAC
upper sequence: AT1G73010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01430.1 (Glycine max), 3'ss of exon 2
gtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtcta-acaatattttttttctattaaaatatgtctaatg--ttagacaaaacccaccatttctgatccgatatttacgg----gttcg-gtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
|| ||||| ||| || | || || |||| ||| | ||||| || | | | || || ||| | | | || || ||||| || || | ||||||||||||| | ||||| ||||| ||||||||| |||||||||| ||||| || | | || | ||||| || ||| ||| || ||||||||| | |||
----------------------------------gtatgtaattat-gcatctcttatccttacacaaaattctgtttctgttctttttctttttataattttattttaacaatctaaattggagaggaaatttatggtggcatttgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACGTGTTTTTCATTGAGACTATTCTGAAGCACTTGGGAATAAGAGAATACTTTTCAGAGATCAACACCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
ttctgat putative branch site (score: 3)
atattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtctaacaatattttttttctattaaaatatgtctaatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA