Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatctttgtggccttggtttacttcccctgtcttctttttttcgaatttgtgttgatgattgttccatcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G28240.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------gtgagtatctttgtggccttggtttacttcccctgtcttctttttt-------------tcgaatttgtgttgatgattgt-----tccatcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
|| | | | || ||| | ||| ||| || | || || | || | ||||| ||| || |||| ||||| | |||| || ||||||| || || |||||||||||||| ||||| | ||||| ||||||||| ||||||||| ||| |||||||||| |||
gtatgtttcgtgatttgttggatgtttcccttctgtatatctatgagtactgaagaaggttgtttgtggttataatttgtttgtttcagtaataacggt--atttctcctatccttttacttacatctgtccatgctgcatctacaatgatgcatgtgtacatcattcagATTTGTTAGAGGAACTAAACCTGGCCGCAACACAGGATTTGACATGGATGAAGATGATCTCCTTGAAATGGAGCAGTGTCATGGTGTAGTTGTTGCATCA
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G24770.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------gtgagtatctttgtggccttggtttacttcccctgtcttc--tttttttcgaatttgtgttgatgattgt-----tccatcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
| |||| | | |||| | || ||| | | || || || | | |||| ||| | ||||| ||||| | |||| | |||||||||| || |||||||||||||||||||| || || | | |||||||| |||||||| ||| | |||||||| |||
gtatgttttgctttttgttgaatgtttcccttacttataagttacatctatacccactgaggaatgttctttgtggttataattgtccgtgctagtaattaagcattcttg-tacctttttactgacatgaattcattctccatcttcaataatgaatgtgtataccaatcagATTTGTTAGAGGAATTAAACCTGGTCGCAACACAGGATTTGACATTGATGAAGCTGACCATTTTGAAATGGAGCAGTGTAATGGAGTGGTTGTTGCATCA
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G31680.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------gtgagtatctttgtggccttg-gtttacttcccctgtcttctttttttcgaatttgtgttgatgattgttcca-tcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
| |||| | | |||| || ||| | || || || | | |||| | | ||| |||| ||||| | |||| | ||||||| || || ||||||||||||||||||| || || ||| |||||||| |||||||| ||| | |||||||| |||
gtatgttttgctttttgttgaatgtttccctaataagtaacatctatacccaccaaggaatgttctttgtggttatagttgtctgcgctagtaattaagcattcttgtaatttcttactgacatgaattcattctccatcttcaataatgaatataccaatcagATTTGTTAGAGGAATTAAACCTGGCCGCAACACAGGATTTGACATTGATGGAGCTGACCTTTTTGAAATGGAGCAGTGTGATGGAGTGGTTGTTGCATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttacttcccctgtcttctttttttcgaatttgtgttgatgattgttccatcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
tgttgat putative branch site (score: 4)
ttgttcc putative PPT
tttttttcgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatctttgtggccttggtttacttcccctgtcttctttttttcgaatttgtgttgatgattgttccatcagGTTTGTCAAAGGACCTCAACCTGGTCGAAATACAGGATTTGACATTGATGAGGCAGATCTTCTTGAAATGAAGCAGTGTCGTGGGATAGTTGTTGCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC