Sequence
atgc intronic sequence ATGC exonic sequencegcaagtggtgtatgatatgatgaatcttattggttattttgacactaacggtgtccatacaatttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 18
-------gcaagtggtgtatgatatgatg-aatcttattggttatt--ttgacactaacggtgtccatacaat--ttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
| | ||| | ||| | ||||| | || |||| ||| | | | | || | ||| | || || || ||||| ||| | || |||||||| || || ||||| ||||||||||||| ||||||||||||||| || |||||||| || ||||
gtatggaactatcattgtcttctataacatggaattattaatatttgattgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 18
-----------gcaa-gtggtgtatgatatgatgaatcttattggttattttgacactaacggtgt-ccatacaat-ttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
|| || | ||| | ||| | | ||| | || || ||| | | | | ||| || ||| | || || || ||||| ||| | || |||||||| || || ||||| ||||||||||||| ||||||||||||||| || |||||||| || ||||
gtatgaaactatcatcgtcttctataacatgg-aattattaatatttgattgataactgaaaacttactaactaatatttagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 19
-------gcaagtggtgtatgatatga--tgaatcttattggttattttgacactaacggtgtccatacaatttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
| ||| | ||| | || | ||| || || || || || | | | || |||||| | || || || ||||||||| | ||||||||||| || || || || |||||||| || | |||||||||||| || ||||||||||| || ||||
gtatggtggtgtcattgttttctataacttggaacttcttaaataattgttgacaaa--gctttcgtatgtgttcagGTTGCTAAAGAATATTGTGAGCAATTGGGTGTTGATGCCTGCATAAAACTTTTTGAGCAATTTAGGTCATATGAAGGACTGTACTTTTTCCTTGGATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatgatgaatcttattggttattttgacactaacggtgtccatacaatttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
cactaac putative branch site (score: 1)
ttattggttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtggtgtatgatatgatgaatcttattggttattttgacactaacggtgtccatacaatttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG