Sequence
atgc intronic sequence ATGC exonic sequencegttatttccctgttccagactttgatcataaactctcctttttcttttatatggagcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24430.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 8
gttatttccctgttccagactttgatcataaactctcctttttcttttatatggagcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagt--agGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
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----------------------------------------------------gtgtgtccacaatgtgatgcattatacaagtct--agcgtataaatctaaccttacattgactagtttctgtatcctcttctgtcgccaagGTTCCTTGTGTTGCGGTTGTAGAGAACATGTGCTATTTTGATGCTGATGGAAAACGTTATTACCCATTTGGACAAGGTTCTGGAACTCAG
upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------gttatttccctgttccagactttgatcataaactctcctttttcttt-----tatatgga-gcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
|| |||| | | | ||| | | | | | | ||||| | ||||||| | ||| | | | || || || | | | |||||||| |||||| | | || | |||||||||| ||||||||||||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| | ||||||||||||| ||
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatactt-catttgatacttacatttattttttgtttgttaatgcgta--agGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
----------------------------------------------gttatttccctgttccagactttgatcataaactctcctttttcttttatat-------ggagcttgtgaacttgttt-ttcttctcaactctgc--aacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
| | | || || | | || || | | || | | | || ||||| | |||||| | ||| | || | ||| | | || | | | | ||||| || || || || | | | |||||||||| ||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||||| ||||| | ||||||||||||| ||
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctg--ttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
gttatttccctgttccagactttgatcataaactctcctttttcttttatatggagcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
|| | || | | || |||| || | || | | || | | | | || ||| ||| | || || | | || ||| ||| || | |||| || || ||||||||||| ||||||||||| |||||||| |||||||| || || |||||||| ||||| | |||||||| ||| ||
-----------gtacttgattcttattataa----tcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaa-tatctactaattctcttgacacattc---gttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
agatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatttccctgttccagactttgatcataaactctcctttttcttttatatggagcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT