Sequence
atgc intronic sequence ATGC exonic sequencegtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgcaatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
-------------------------------gtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgc--aatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
|| | |||| | || | | | | ||| | | | || | ||| | || | || | | |||| || ||||| |||||||| || ||| | || || || |||||||| ||||||||||||||||| || || ||||| ||||||||||||||||||||
gcaagcattatgttatactctgagcaatcctttgtcctcttctacc-ccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G03810.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgcaatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
|| | | | | || | | | | | | | | || | | ||| | || | | | |||| |||||||| |||||||| || ||| | || || || || ||| | ||||||||||||||||| || || ||||| |||||||||||||| |||||
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctacttctcacattagaatc-gtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 3'ss of exon 4
gtgattttttctgcggt--tttatggttttg-ccttttg-gacaaatgtt------tggtaagtatcggatttaagaaagaataaaaatgcaatg-gcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
|| ||| || |||| ||| || ||| || | ||| | || | | | || | | | || | | | ||||| || ||||| ||||| |||||||| ||| ||||| || || ||||| ||||| ||||||||||||||||||||||| |||||||||||||| || ||
gttgtttccagtgtaacagtttagagttgtgatcttctgtgttaaacatcacagaatgagagatcttcaatgctaatattgttgaattttctacctgcagGGGTTACAACAATTGCAGGGGGGAAGCTGGGCCGTGGAGGGGGGCATGTAGATGGGCCAAGTGAAGATGCAAAGTTTTCTAATGATTTTGATGTGGTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgcaatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
atttaagaaagaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgcaatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG