Sequence
atgc intronic sequence ATGC exonic sequencegttagtttcatcaaagttgcttctttgtgttttctcctacaacaaattcttgatttatagaaaccaataatagGATCCTCTAAGAGCAAGTGACAAGCCTTTAACAAGCTGTGGTCCTTACAAAATGAAAGAAGACGATGCAATGGTTTATCGAAGACCTTATCTTACCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12830.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12830.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G23870.1 (Glycine max), 3'ss of exon 10
------------------------------------------------gttagtttcatcaaagttgcttctttgtgttttctcctacaac---aaattcttgatttatagaaaccaataatagGATCCTCTAAGAGCAAGTGACAAGCCTTTAACAAGCTGTGGTCCTTACAAAATGAAAGAAGACGATGCAATGGTTTATCGAAGACCTTATCTTACCTCAG
||| | | | || | |||| | | | | | | || | | | | || | ||||||| |||| || |||||||| || ||||||||||||| || || |||||||||||||| ||||||||||| ||| ||||||| |||||||| || |
gtacaaaatgttcatacatattaatgatgttctaatattcagattttatttatatctacttgaattaatagtttggatggccccaaaaggcttgagatgatacactgctcttctgcatgatcagGATCCATTAAGGGCCAGTGACAAAGCTCTAACAAGCTGTGGCCCCTATAAAATGAAAGAAGAAGATGCAATGGTCTATAGAAGACCCTATCTTACATCTG
upper sequence: AT4G12830.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv07s0151g00860.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------------------------------------------------------------------------------------gttagtttcatcaaagttgcttctttgtgttttctcctacaacaaatt--cttgatttatagaaaccaataatagGATCCTCTAAGAGCAAGTGACAAGCCTTTAACAAGCTGTGGTCCTTACAAAATGAAAGAAGACGATGCAATGGTTTATCGAAGACCTTATCTTACCTCAG
||| || || | ||| || | | | | || |||| | || | | || ||||||||||||| || || || || |||| || ||||||||||||||| |||||||||| || ||||||||||| ||| |||||||||||||||| || |
gtaggaaagctacagcacagaatttgaattattatcattcatatacatgcacacacatttttgactgagttaatgggtgcttgtacacgtgtgtacattcatatgctttcttagtttgtgatgtccagattgattgcagaccataacaaacatgattgatgaacttgtgctttatatcc---tatcagGATCCTCTAAGGGCTAGCGATAAAGCTTTGACGAGCTGTGGTCCTTACCAAATGAAAGAGGATGATGCAATGGTGTATAGAAGACCTTATCTTACATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttctttgtgttttctcctacaacaaattcttgatttatagaaaccaataatagGATCCTCTAAGAGCAAGTGACAAGCCTTTAACAAGCTGTGGTCCTTACAAAATGAAAGAAGACGATGCAATGGTTTATCGAAGACCTTATCTTACCTCAG
tcttgat putative branch site (score: 4)
aaattcttgatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttcatcaaagttgcttctttgtgttttctcctacaacaaattcttgatttatagaaaccaataatagGATCCTCTAAGAGCAAGTGACAAGCCTTTAACAAGCTGTGGTCCTTACAAAATGAAAGAAGACGATGCAATGGTTTATCGAAGACCTTATCTTACCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA