Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgtaataatatccccaattgcattcttttggttgtatcaatttttgttcttgcataaatgtgtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 2
------gtacgtgtaataatatcccca---attgcattcttttggttgta-tcaattt---ttgttcttgcataaatgtgtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
| || | ||||| | || ||| | | || || || | || | | |||| | || || | | | || | | |||| | || | | | ||| || ||||| ||||| |||||||||||||| || || || ||||||||||| ||||||| |||||| | ||||||
agagcagaaccttgcataatttttacatagatttcctgctcctgcttccggttcatgtacactattctagtattcatctctacttttacttgcgcgcca-gGAAAAGGAAGCTGCGCTCACTGAGTTTCAGGCTCTGGACTTTCCCTGTTCTTGTAGACGGCCCCTTTGGAGTTGTCTCTGCAGTTGAGTTCATCGGAATT
upper sequence: AT5G49730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G13090.1 (Glycine max), 3'ss of exon 2
--------gtacgtgtaataatatccccaattgcattcttttggttgtatcaatttt-tgttcttgcataaatgtgtgtgtcatgatgattgtga----agGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
| | ||| | || | ||| ||| | || | | | | | | | | ||| | | | | || ||| |||||||||| || ||| | || |||||| | ||||||||||| ||||| |||||| | ||||||||||| ||||||||||| | ||| || |||| |||
ttgaagttgcggccgaaattgcggtcacaggcggatt-tttaaaacatgacattatagtatatgttgagtactttgtttttgacttgggttttgatggcagGAAGAAGACGTCCAAACTTCCAAGGTTTCGCCTATGGACATTTCCTGTGCTTGTGAAGGGACCATTTGGGGTTGTTTCTGCCACAGAGCTTATTGGGATT
upper sequence: AT5G49730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g02150.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------gtacgtgtaataatatccccaattgcattcttttggttgtatcaatttttgttcttgcataaatgt-gtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
| ||| | || | | || |||||| | || | | ||| || | | | | | | || || | ||||||| || || || | || || ||| || | ||||| || |||||||||||||||||||| |||||||| || ||||| |||||||| | || ||
gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataatagttgtcctagttttttctttctcatcatataaaactttggttat--agGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttgtatcaatttttgttcttgcataaatgtgtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
tatcaatttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgtaataatatccccaattgcattcttttggttgtatcaatttttgttcttgcataaatgtgtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA