Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgattttctaggagcatgtcttaaacttctccggttctccctaatccttggggtagaggtgcaagattacgtgatttcttgaaaacaaaatataacaggctgaatcgttctctgtttcttgattgtgtatgatgtcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63960.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 21
--------------------gtaagtgattttctaggagcatgtcttaaacttctccggttctcc---ctaatccttggggtagaggtgcaagattacgtgatttcttgaaaacaaaatata-acaggctgaatcgttctctgtttcttgat-----------------tgtgtatgatg-------tcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
|||| || | || | ||| | || | || | || |||| ||| | | | || ||| || || ||| | || || | | ||| | | | |||| || || | |||||||||| | |||||||| ||| |||||||||| ||||| || |||| ||||||||| |||||||||||| |||||||||||| | | |||||||
gtgactcattaactactgtggtaactgttatttgacattaatgcccctccgtttcaaaatcatctgaaatgatacttgtcgtaataattttgccctttgcatttcctttctaattttgcatctgcagtatccattttttttccaattttgttactttgagttcaactcatatttatgttgatacctttcctgcagCCCATCAAGCTTGAGTTTGAGAAGATCTATTTCCCTTATCTACTGATTAGCAAGAAGAGATATGCTGGTTTGTACTGGACAAATCCTGAGAAATTTGACA
upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 5
gtaagtgattttctaggagcatgtcttaaacttctccggttctccctaatccttggggtagaggtgcaagattacgtgatttcttgaaaacaaaatataacaggctgaatcgttctctgtttcttgattgtgtatgatgtcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
| | ||| ||| || || | | | | | | | | | | | | | ||| || || | || | ||||||||||| |||||||||| ||||||||||| || || ||||| || | ||||||||| |||||||||||| ||||| |||||| | | |||||||
--------------------------------------------ttcacacgttgcaaaagatttgtaacgtatccagctaagctttcatttgcttttcat---ttaagtttcaattcacacgttgcttatgacatctttctcacagCCCATCAAACTGGAGTTTGAGAAGGTCTATTTTCCTTACCTTCTAATCAGCAAGAAGAGATATGCTGGTTTGTACTGGACGAATCCTGAGAAATTTGACA
upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA06G16110.1 (Glycine max), 3'ss of exon 21
gtaagtgattttctaggagcatgtcttaaacttctccggttctccctaatccttggggtagaggtgcaagattacgtgatttcttgaaaacaaaatataacaggctgaatcgttctctgtttcttgattgtgtatgatgtcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
| || | | | || || || | | | | ||| || || | | | ||| | || || | | || |||| | | | |||||||||||| | || ||||| ||||| || | |||||||| || |||| ||||||||| |||||||||||| | |||||||| || | | |||||||
-------------------------------------gagacttcattcttgtttaagtgt--gtttgaagtcaactaattattttaa-------ttttttactttgatttgtcct-tacgtatttgttgtcattttgattgtgaagCCCATCAAACTAGAATTTGAGAAGGTTTACTATCCATATCTCCTGATTAGCAAGAAGAGATATGCTGGTTTGTTTTGGACAAAACCAGACAACTTTGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatataacaggctgaatcgttctctgtttcttgattgtgtatgatgtcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
tcataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgattttctaggagcatgtcttaaacttctccggttctccctaatccttggggtagaggtgcaagattacgtgatttcttgaaaacaaaatataacaggctgaatcgttctctgtttcttgattgtgtatgatgtcataaagCCCATCAAATTGGAGTTTGAAAAGGTCTATTTCCCATATCTTCTCATTAACAAGAAGAGGTATGCTGGTTTGCTATGGACAAATCCTCAACAGTTTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG