Sequence
atgc intronic sequence ATGC exonic sequencegtttgtccactttatcattaccatacatcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73450.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 4
---------------------------------------gtttgtccactt-tatcattaccatacatcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
||||| | || || || || | | | | | | || || ||| | | |||||| || |||||||| |||| |||||||| || | || |||||||| ||||| || || || || ||||||||||||||||| || || |||||||| || ||||| |
gtattactgagctaggttatccactaatgttgacttattgtttgactaccagtaacaaaacacgattctacaatttttcacatagatttgatatttt-tttctttgttgtaccccttggcagTCAATAGCTATTCAGTGTCTGGAGGCGCTGCAGTTTCTGCATGGTCTCGGTCTAATCCACTGTGATTTGAAGCCAGAAAACATATTGGTAAAGAGCTACA
upper sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtttgtccactttatcattaccatacatcatagatatgtatatg-tatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
|||||| | | ||| ||| | |||| | | | || | | | | |||| || | ||| |||||||| || || |||||| | ||| ||||||||||| | || | |||||||| ||||| ||||| |||||||| |||||||| ||||| ||||||||||
gttagtgctgtgctgtgatatgttctttctatatttacttatcatgctgtttgtac-tgtgatctttagttttcatcctttctgctagtgcaatactgtcattataaacacttttcaacttatgtgtgcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCAGAGAATATTTTGGTTAAAAGCTATA
upper sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtttgtccactttatcattaccatacatcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
|||||| | | ||| ||| | |||| | | | | | | || | | | |||| || | || |||||||| || || |||||| | ||| ||||||||||| | || | |||||||| ||||| ||||| |||||||| |||||||| ||||| || |||||||
gtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtac-tgtgatctttagttttcatcctttctgctagtctaatactg--tcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
upper sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 10
-----gtttgtccactttatcattaccatacatcatagatatgtatatgtatccgattcctgatct-ctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
| | || ||| | | || || || | ||| | | | | | || |||| | ||||||| ||||| || || || |||||| | || |||||||||| | |||||||| || |||||||| |||||| |||||||||||||||| |||||||| |||||||
gttatggagttacatttttaaactgatatctttctctcctactgacatg---ctggtatgtaacctgcttttaaattgttctgtgcagTCCATTACAATTCAGTGTTTGGAGGCACTTCAGTTCTTGCATGGCCTAGGCCTTATACATTGTGATCTGAAGCCTGAGAATATTTTGGTGAAGAGCTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
tcctgat putative branch site (score: 3)
ccgttct putative PPT
atatgtatatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtccactttatcattaccatacatcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC