Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctttttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16155.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 6
----gtaagcctttttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
|| | || | || | || || | || | | || || | | || | || ||||| | | || ||| |||| ||||||||||||||||| ||||| |||| |||||| || |||||||| ||||| ||||||| ||| || || | |||
gttaactagaccttctacctta-gctttcttcataccgcagacacatttcatcatc--tctatg--ttaaaattgttgatgattttttctagATTACTCCAGCAAAGGATGGAAAACCTGTGCAGATTGAGCTCATTGATGCAAAAACAAAGGAACACAAAGAAACCCTCGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 6
gtaagcctt---tttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
|| | | | || |||| || || | || | || || || ||| | || | || | | ||| |||| || |||||||||||||| ||||| ||| ||||||| |||||||||| || || ||||||| |||||| || | |||
gttaccttgagattcaactcaagctttctccataatatgaaatcttttgacacta---ttgtaaccttgcaacatccatatctct----agATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 6
---gtaagcctttttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
|| || | | | || | | |||| | || | || || ||| | | | |||| | | || ||||||| || |||| |||||| ||||| || |||||||||| |||||||| ||||||||||| || || || || |||||
gtaacaacatcttgtaatttcttgatataattttagttggctac--tatgacatg---ctacacagtcctcatgtt-----tgttgtatagATCACGCCTGCAAGGGATGGAAAACCTGTCTTGATTGAACTTATTGATGCGAAAACCAAGGAGCCGAAAGACACGCTGGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 6
gtaagcctttttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctt-tacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
| | ||| | || | || ||| || ||| | | | | | | | | | || || || ||||||| || |||| |||||||||||| || |||||||||| |||||||| ||||| ||||| || || || ||| |||||
----gtaacaatatcttgtaatttcttgat---ataattttattatttggctactatgacatgctacagtcctcatgtttattgtatagATCACGCCCGCAAGGGATGGGAAACCTGTCTTGATTGAACTTATTGATGCAAAAACAAAGGAGCCAAAAGACACTCTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
tgttaac putative branch site (score: 2)
cgcttcttt CT-rich tract
tttacgaatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctttttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG