Sequence
atgc intronic sequence ATGC exonic sequence...agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaattttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 13
-agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaattttacattttcttgatattctttttttt-tttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
||| || || | | | | | | | | | |||| || || | || | | ||| | |||||||| | || |||||||||||||||||||||||||| ||||| ||||| ||| | ||||||||||| ||| ||||||||||||| || ||||| |||||||| || || || |
cagatttggttggactttatttgtaaggtgcatgatgccactatcatgatgattttttttct--ttctcaatatcttaaatagtattttttttgtcttgcagGCCATTGATGCAAGAGATGCTTTGGCAAAGTCAATATATGCATGCCTGTTTGATTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGAC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 11
----agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaatt--ttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
||| | | ||| || || ||| || |||| | | || | | ||| || || || | | | || ||||||||| || ||||| |||||||||||||||||||| ||||| ||||| ||| | ||||||||||| ||| ||||||||||||| || ||||| |||||||| || || || |
tggtagaatgtaggttc-----aataccttgaatg-atttggaaatagatgtttataatgattttttttctttccaaatatcttaaatattttttttttcttgcagGCAATTGATGCAAGAGATGCTTTGGCAAAGTCAATATATGCATGCCTGTTTGATTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGAC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 13
agacttttaattcctccgaagacgatgattgtatttttag--tcccgtccttc---ttttactttaaattttacattttcttgatatt--ctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
| | | | || || |||| | || | | | | ||| |||| | || ||| || | |||| | ||||| || | ||||| |||||||||||||||||||| || || ||||| ||| | || |||||||| ||| |||||||||| || ||| |||| ||||| || || || || |
-------acacttcattggtgatgaacattgcttcattggattttccttcttggaattttcactcaatcgttaaatatgaatgattgttgcttttcttatcacgcagGCTATTGATGCAAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACCAATCCCTTGCGGTTGGCAAAAGAC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 11
agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaat----tttacattttcttgatatt--ctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
|| | | | | | |||| | || | |||||||| | ||| | | || || | |||| | ||| | || | | |||| |||||||| ||||||||||| || || ||||| ||| | || |||||||| ||| |||||||||| || |||||||| || || || || || || |
-----gaaaacttcattggtaatggacattgcttcattggattt-tccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
---agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaattttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
| |||| | | | || | || | | || | | | | ||| | | ||| | | | || | |||| | || ||||||||||| ||||||||||||| || |||||||| ||| | || | |||||||||||||| ||||| |||||||| || |||||||| ||||| |||
gtctaatttttgaat--ttggagtaacttggataaaattccacggatatttgtaagacattttcccctatg-attattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttcttttactttaaattttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
tcttgat putative branch site (score: 4)
ttttacattttcttga CT-rich tract
tttaaattttacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaattttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG