Sequence
atgc intronic sequence ATGC exonic sequencegttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaattaaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 6
gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaat--taaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
| | | || | | | | ||| | || | || || | | || ||| | | ||||| || | | | | ||| || | || ||| | | | | || || ||| ||| ||| | |||| | | ||||||||||| || ||||||||||||||||| |||||| || |||||||| || | || | |||
----------gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaa-atttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttg-taattcgatttggttttc----cttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 6
gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaattaaagggttttcagttacctaatccaatttactaagaatgttttatttata--taattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG-
| ||| | ||| | | | || |||||| | || ||| | | | | || | ||||| | ||||| | ||| | | | |||| | |||||||||||| || ||||| || ||||| || |||||| ||||||||||||| || |||| | |||
-------------------------------------------------------------ttttaggatcaaatttattatcatc--agtcatagaaatttcaattt------tttgctgctgcata-tataatttcaaagttatgttgtttttgttgtttctcacaggAAAATCTGGTTGGGCTGCCCCTCGTCTTAAAGATGCAGCTTTATCTTTAGACAAGTTGCGGGAAGGCTATGTTGAGG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 6
gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaattaaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
|| ||| | ||| | | |||| | || | || || | || || ||| | | | | | | |||||| || | | | |||| | |||||||||||| || ||||| || ||||| || |||||| ||||||||||||| || |||| | |||
---------------------------------------------------------------ctgcatatatcatttcattctggtaatgcagactattgtttaagtagaaa--ttacaaataca-attttattgaagttctgttgtttttgttgtttc-tcacagGAAAATCTGGTTGGGCTGCGCCTCGTCTTAAAGATGCAGCTTTATCTTTAGACAAGTTGCGGGAAGGCTATGTTGAG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 6
gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaattaaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
| | | | ||| | | | | ||| | || || | ||| || || | | | || || | || ||||| | |||| | || |||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||| || | || | |||
-------------------------------------------------------------ggtttccattaaaaaagtatggaatttggaatttggaattttaaaaaaatgtttttacatctaattgttggagttctcttggtg-attgtatttgt-----cacagGAAAGGCAGGTTGGGCTGCACCTCGTCTTAAGGATGCTGCTTTATCTCTTGACAAATTGCGTGAAGGTTATGTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
acctaat putative branch site (score: 3)
taatccaatttactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaattaaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC