Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttcatatgactggcttcgtcatatattgtgaagtaatacaacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------gtatgctttc-atatgactggct---tcgtcatatattgtgaagtaatacaacattatcgatca---------tttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA
| || ||| |||| | | | || |||| || | || | || || | | ||| | ||||| | | |||||||||||| || ||||| ||||||||||| |||||||| || | || | ||||| | | | ||| ||||| || |||||||| || || || |||||
gtaactagcaagtcatattctttttttcccttttctatttcataatttaaataatcctccatgtggtttggatatcaaggagcagaaagaaatgtattaggattttgtagatgtttttcaagtaacatgtgcttttctttatcttt-tatatgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAGATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------gtatgctt-tcatatgactgg------cttcgtcatatattgtgaagtaatac--aacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA
|| || | |||| | || | | | || |||| | ||| | | | | ||||| | ||||| | | |||||||||||| || ||||| ||||||||||| |||||||| || | || | ||||| ||| | ||| ||||| || |||||||| || || || |||||
gtaattaccaatccatattgttttttcttttctatttcttaatttaattaatgcatgtggtttggatatcatggagcaggaggaaacataggtggattttgtagaaaaatttcaagtaacacggtgcatttctttatcttt-tatatgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAAATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 10
gtatgctttcatatgactggcttcgtcatatattgtgaagtaatacaacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA--
| ||| || || | | | | ||| |||||| || || || || |||| ||||| |||||||| |||||||| ||||||||||||||| || ||||| | ||||||||| || | ||||| ||
--------------------------------------------gtta-attgtctgacagctccttttattgttacta--agagGAGTACATTGGGTTAGATGCAAACAAATATATTGGGGATCTCCTGGCAGAATTTAAAGCTGCAAAGGATCGGAGTAAAGGAGAAATCTTGCACTGTAAAC
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 7
gtatgctttcatatgactggcttcgtcatatattgtgaagtaatacaacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA-----------------------------------------------------------
|| | || || || || ||||| |||||||| |||||||| ||||||||||| || | || ||||||| ||| ||||| ||| | ||||||||
---------------------------------------------------------------------------------------gtacgttgggttagacgacaacaaatatattggggatctcctggcagaatttaagGCAGTGAAGGATCGAAGTAAGGGAGAAATATTGCACTGCAAACTAATTTTCAAGAAAAAGTTATTTCGTGAATCAGATGAAGCTGTGACAGATCCAATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattgtgaagtaatacaacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA
taatacaacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttcatatgactggcttcgtcatatattgtgaagtaatacaacattatcgatcatttttctatctgtgcacttgcagAGGAATATATAGGATTGGATGATAACAAGTATATTGGAGATCTCCTCGCAGAATTTAAAGCTATTAAAGATCGAAATAAAGGAGAGATACTACACTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA