Sequence
atgc intronic sequence ATGC exonic sequencegtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00630.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 3
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataa---tgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctat-agGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
| | | | || || ||||| ||||| | | ||| || ||| || | || | || | | || | | |||||| ||||||||||| ||| | || || || || | |||||||| ||||| ||||| || || |||||||||||||| || ||||| ||||| |||||
--------------------------------------------------------------------------------------atgtgcatacaaaagttgagaaacatctgtgattaagatcatcagttttcatggaagtttttgtgaccttctgcaaataaattttaccttgatatcttagGCAGTCCTGTTCTTGGATATCTTGCTGCTGGTGTCCTCATTGGTCCATATGGGCTCTCCATCATCCGTAATGTGCATGGGACAAAGGCAATTGCGGAATT
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 3
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
| || ||| || || | | || | || |||||||| | ||| | || | || | | |||| |||| | ||||||| ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| |||| |||||||| || || || || || ||
---------------------------------------------------------------------------atcat-catctgaattatgttttgggatacaggatttatttta----aatcataacttgatcaaattgattgtctgacaagtcatctac--ctgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCCATCATTCGTCATGTTCATGGAACAAAAGCAATAGCCGAGTT
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 7
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
|| | ||| | | | || | || | | | || | | | | | |||| |||| | | | | ||| |||| | ||||||| ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| | || ||||| || || || | || |||||
--------------------------------------------------------------------------tatgttaaatttcttttaa-aggtatactcgataaaattaactgtc-------ttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 11
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
| || | || | || | | ||| ||| ||| |||| ||| || | | || | ||| ||| | || | ||| |||| | |||| || ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| | || ||||| || || || | || |||||
-------------------------------------------------------------tgtgttaaatttct----tttaaaggtatactcaataaaattatttgtcttacattcacatttttttaccg-------------atgttattccctctgtct----tgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 2
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
| | || ||| ||| | ||| || || | | | ||||| | | | | ||| | || || ||| || | ||||||||| | | ||||||| ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| |||| ||||| ||||| || |||||||||||
---------------------------------------------------------------------gcatatatatgtcactgt-gccttcattt---cctttcaaagtttattgcca-agtttctgtact-----gtttcattgatagtgtgtc--ttccatctgctgca-tgtttagGCAGTCCTGTTCTTGGTTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATTATTCGTCATGTACATGGGACCAAAGCGATTGCAGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
atagagatttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA