Sequence
atgc intronic sequence ATGC exonic sequencegtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61150.2 |
intron # | 4 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G31720.1 (Glycine max), 3'ss of exon 2
gtatcctttttctgattctggtt--ttgagtttttgtttatggaattg-gtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
| ||||||||| | | | | || || | ||| ||| ||| | | ||| || || | | | | ||| |||||||| || |||||||| ||||||||||| || || || ||||| ||||||||||| || || || |||| || ||||| |||||||| ||||||||||| ||||| || ||
gcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAGTACAAAGTGGTAATGTTGAGGATGCAATTGAAAAAGTGAATGACTTAAA
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA---
||||||||||| | | ||| || | |||| | ||| || | | ||| || || | | | | ||| |||||||| || |||||||| ||||||||||| || || || ||||| ||||||||||||||||| || |||| || || || || ||||| ||||||||||| ||||| || ||
gtatccttttttttaatctatttatttgtttatttttg-ggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
||||||||||| | | ||| || | |||| | ||| || | | ||| || || | | | | ||| |||||||| || |||||||| ||||||||||| || || || ||||| ||||||||||||||||| || |||| || || || || ||||| ||||||||||| ||||| || ||
gtatccttttttttaatctatttatttgtttatttttg-ggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
gtatcctttttctgattctggttttgagtttttgtttatgg-----aattggtgtgtttgatgtttagcttatctactccttttgaactt--ccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
|||||||||| | || || | || | || || ||| | |||| | | || | || | | ||| |||||| || ||| |||||| ||||||||||| || || || ||||| ||||||||||| ||||| || || || ||||| |||||||| ||||| ||||| |||||||||||
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctttttctgattctggttttgagtttttgtttatgg-----aattggtgtgtttgatgtttagcttatctactccttttgaactt--ccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
|||||||||| | || || | || | || || ||| | |||| | | || | || | | ||| ||||| || ||| |||||| ||||||||||| || || || ||||| ||||||||||| ||||| || || || ||||| |||||||| ||||| ||||| |||||||||||
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcaatttttagctgtaaagcttattcttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S268_9V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactc----cttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
|||| || | | ||| ||| | ||| | | | | | | ||| || | | ||||||| |||| ||||||||| |||||||||| ||||||||||| || ||||||||| ||||||||| || ||| | || || ||||| || || ||||| ||||| |||||
---ctgaacgaatgatgctaatgatcagtga--aattaaagggttgtgttactcattctgaaattctcttacagtgggctggtccaattccttagcgaggaacagCAGACATAGATCTTGGCACCATTACTGACCGCATGGCTGTTCGAAAGGCTGTACAGTGTGGACAGGTGGAAGATGCTATCGACAAAGTCAATGACTTGAA
upper sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S379_20V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtt-tagcttatctact--ccttttgaac--------ttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
||| | || | | | ||||| || | | || | |||| ||| || | | | || | | ||| || ||||||| |||| ||||||||| |||||||||| |||||||||||||| |||||||| ||||||||| || || | || || ||||| || || ||||| ||||| || ||
---------gtctaaacgtg---tgatggtattgttcatagtactgaaatctttgtcgttctaaatgaaattctgacatattggaccgatctagttccttagcgaggaacagCAGACATAGATCTTGGCACCATTACTGATCGCATGGCTGTACGAAAGGCTGTGCAGTGTGGGCAAGTGGAAGATGCCATCGAGAAAGTCAATGACTTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
ttccttatc putative branch site
cttccttatc putative PPT
atgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG