Sequence
atgc intronic sequence ATGC exonic sequencegttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaactatagtgccatgtgactggattctaaatttttattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45030.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 9
---------------------------gttagttg--aagtttatttttctccttaagattccattatggtagctccgtggtg-gcaactatagtgccatgtgactggattctaaatttt-tattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
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gtaagttgcaccagatgttgtaaccaaaataattactaagtattagtttgatctgatcattggagttgattgtttcctttataagcaaatccacccctaggctaatatcttctttattctgtggtcaatat--agGATATTCAAGAAGCACATGCTGGTCAAATTGTTGCTGTCTTTGGTGTTGATTGTGCGTCAG
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 9
gttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaacta-tagtgccatgtg-actggattctaaatttttattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
|| ||||| | | |||| | | || | || | | | || | | | | || | | | | || ||| || | | | ||||||||||||| ||| | ||||| |||||||| ||||| |||||| |||| ||||||||||
gtaagttgcattagatttagttttcactcaatcagtattgatttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S100_33V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------gttagttgaagttta---tttttctccttaagattccattatggtagctccgtggtg-gcaactatagtgccatgtgactggattctaaatttttattctat-tttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG---------------------------------------
|||| | || |||| | | | | | || || || | | | | || || | || || || || | | | ||||||||||||||||| |||||||||||| ||||||| || || |||||| |||| ||| | || |
gttagttttggtcttgtctttacgttggaattatgggtcggagttaatctggtttcggaccttttagcgtctggttgctgttgtgctacattcttattctataataatcatctca-atggtctttttttactccgtggacttgtgtttcagGATATTCAAGAAGCACACGCTGGAGAAATTGTTGCAGTCTTTGGTGTTGAATGTTCTTCTGGTGATACCTTTACAGATGGATCTGTAAAGTACACTATGA
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------gttagttgaagtt----tatttttc--tccttaagattccattatggtagctccgtggtggca-actatagt----gccatgtgactggattctaaatttttattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG---------------------------------------
| | || || | |||| | ||| || || | | | || ||| | || |||| ||||| || | | | | | |||||||| |||||||||||||| |||||| ||||||| || || |||||| |||||||| | || |
gttagtctgaatctctctccttgtccttttttttgtttctgttttgtttttgtgggttggtgtatcttttgaaagaatgatcaaacttatgctgcttttaggtttctaaagttgtgttgctggcgtgctgttgtgctacaccgtagttattatcatgtctctacttacattctgcggagttgtatttcagGACATTCAAGAGGCACATGCTGGAGAAATTGTTGCAGTCTTTGGTGTTGAGTGTTCTTCTGGTGATACTTTTACGGACGGATCTGTGAAGTTTACGATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtggcaactatagtgccatgtgactggattctaaatttttattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
ttctaaa putative branch site (score: 2)
tttttattctattttc CT-rich tract
attctaaatttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaactatagtgccatgtgactggattctaaatttttattctattttcagGATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA