Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacatttgattccgaagaaactcttgcagtgtgtgcgtatctgtatacagcctttaactactactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63960.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA04G38800.2 (Glycine max), 3'ss of exon 1
-----gtaaaacatttgattccgaagaaactcttgcagtgtgtgcgtatctgtatacagcctttaactac-tactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
| | ||||||| ||| | | || | ||| || || || || | ||| |||| |||| | ||||||| ||||||||||| |||||||| || |||||||||||||| |||| |||||
gtcagctgtagtgtttgattaattctaaatttactaactgaat-----tctacatgttatctctacctgtacatgatttctctccatatt-tctacttcagGAGGCCAAGGATCCCCTGGAGAAGGCAGTGCTAGATGGTAGACAGCTAGCCCTGAAG
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 17
----------gtaaaacatttgattccgaagaaactcttgcagtgtgtgcgtatctgtatacagcctttaactac-tactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
| | ||||||| ||| | | || | ||| || || || || | ||| |||| |||| | ||||||| ||||||||||| |||||||| || |||||||||||||| |||| |||||
aagctgtcagctgtagtgtttgattaattctaaatttactaactgaat-----tctacatgttatctctacctgtacatgatttctctccatatt-tctacttcagGAGGCCAAGGATCCCCTGGAGAAGGCAGTGCTAGATGGTAGACAGCTAGCCCTGAAG
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA06G16110.1 (Glycine max), 3'ss of exon 17
-----------------------------------------------------------gtaaaacatttgattccgaagaaactcttgcagtgtgtgcgtatctgtatacagcctttaactac-tactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
| | ||||||| | ||| || | || || ||| ||| || | || | ||| |||| |||| | ||||||| ||||||||||| |||||||| || |||||||||||||| | || |||||
gtatcctttctgtacttgttgtgaaaattgactttggatttggattattgaactgtcagctgtagtgtttgattaattaaaaattcactaactgagt-----tctatatgttatctcttcctgtacatgatttctctccatatt-tctacttcagGAGGCAAAGGATCCCCTGGAGAAGGCAGTGCTAGATGGTAGACAGCTGGCCCTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatctgtatacagcctttaactactactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
gtctaat putative branch site (score: 3)
tttaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacatttgattccgaagaaactcttgcagtgtgtgcgtatctgtatacagcctttaactactactattgaaactggtattgtctaatctagGAGGCTAAGGATCCCCTTGAGAAGGCTGTTTTAGATGGTAGACAGTTAGCGTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG