Sequence
atgc intronic sequence ATGC exonic sequencegtatttatactttatgtttactcatgtgcttcaaaatcgttttcgtcaactcgaagacacgggtttcaaagtgaaaaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g29794.1 (Oryza sativa), 3'ss of exon 3
-----------gtatttatactttatgtttactcatgtgcttcaaaatcgttttcgtcaactcgaagacacgggtttcaaagtgaaaaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
| | ||| |||| |||| | | | | || | | | | |||| | | | | || || | || | ||| | | | ||||| ||||||||||| |||||||| ||||||||||| || || ||||| ||||||||||| ||||| || || || || | | |||||||| ||
aaatgctcagggaaaatattctttcagttt--ttactttttctaattttgatacc-tcaagtttagaataaatattcca---ttgaacgcttgctggtagc-tgcagATGTGGAAGATATCCCCCTGTTGTAAGAACAGCTGTTCCGGTGGATGGCAGATTTGAGCACATTGTGCTATCTTGCAACATGATTTCTGATCATGCTATT
upper sequence: AT4G00500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g39580.1 (Oryza sativa), 3'ss of exon 1
-------gtatttatactttatgtttactcatgtgcttcaaaatcgttttcgtcaactcgaagacacgggtttcaaagtgaa-aaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
|||| || ||| | || ||| | | | || ||| ||| | | | | | | || | | || | || | ||| | |||||||| || || || |||| ||||||||| || || ||||| ||||||||||| || ||||| ||||| ||||| ||| ||| ||||||||
tgataatttattaatgttttgt-cttgttcagattact---actcttttgttacaatagagatttccaagcatgatcataaacgaacttgttcctgaattccagGTGTGGAAGATACCCCCCAGTGGTGAAAACAGCTGTGCCTGTGGATGGTAGATTTGAGCATATAGTTCTTTCCTGCAATGCCACAATGGACCATGCCATT
upper sequence: AT4G00500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G085939_T01 (Zea mays), 3'ss of exon 3
-------gtatttatactttatgtttactcatgtgcttcaaaatcgttttcgtcaact-cgaagacacgggtttcaaagtgaaaaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
| | || || ||||| | | ||| | | | | || |||| | | || | |||| || || |||| | |||||||||||||| || || | ||||||||| || || ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||||||
tgatattgaacttgcacagctgttttacatttcttggtcagagtactggttgttgctagtgaagtttccgaaaacacactgaattccttga----aacgcacagGTGCGGAAGATATCCACCGGTAGTCAAAACAGCTGTGCCGGTGGATGGTAGATTTGAGCACATAGTTCTTTCCTGCAATGCCACAGCGGACCATGCCATT
upper sequence: AT4G00500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G01200.1 (Glycine max), 3'ss of exon 3
-gtatttatactttatgtttac-tcatgt-gcttcaaaatcgttttcgtcaactcgaagacacgggtttcaa-agtgaaaaccatg---cccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
| |||| |||| ||| | ||| | | |||| | | | | | || ||| | | | || | | | | || |||||||| ||||||||| || |||||||| || || ||||||||||| |||||||| | ||||| || || |||||||| | || |||||||||
cacaattatg---tatgcttaaattatgaagttatcaaattagatgagcggaatattatctgtatgtagcaataatttggattatagtctcttctgattgtagGATAGGAAGACTTCCACCTGTCGTTAGAACAGCAGTACCTGTTGATGGGAGGTTTGAGCATTTAGTTCTTTCTTGCAATGCAACTTCTGACCATGCCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtcaactcgaagacacgggtttcaaagtgaaaaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
tgccctt CT-rich tract
tttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatactttatgtttactcatgtgcttcaaaatcgttttcgtcaactcgaagacacgggtttcaaagtgaaaaccatgcccttggtatacagATTAGGAAGATATCCACCTGTTGTGAGAACAGCTGTCCCAGTTGATGGGAGATTTGAGCAGATTGTTCTCTCCTGTAATGCAACAGCGGATCATGCCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT