Sequence
atgc intronic sequence ATGC exonic sequencegttggtatactttgttgttgctaaatgctgtcttagtgttttcctatttaaaagaagtgaatatcactgaacattttgctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31410.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G129071_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------------------gttggtatactttgttgttgctaaatgctgtcttagtgttttcctatttaaaagaagtgaatatcactgaacattttg-----ctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
| | ||| | | | | | | | | ||| || || | | | | | | | ||| ||| | | ||||| |||| ||| ||||| | ||||||||||| || ||||| ||||||| |||||||||||||||| ||||||||||||| || | || | |||
gtgaacatttttctttgagaaaagtatgcaatattagcctaaacctacaaagggcatgtttgtaggcttccctttttctatggaaatggaaatgtgaaggatagtactaactaccgagacatacttttttgctcgtgcttattgatgctgactatctttaggt-gttaagcatattgatcttttatctgtagGATTGGGAGGATTTGTGGAGGCCCGAGCTTGCCGGGAGGATTTCAATGGTCGATTCTCCTAGAGAGGTGATTGGTGCTGTTCTGAAGCATCTGGGCTCAT
upper sequence: AT1G31410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08170.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------------------gttggtatactttgttgttgct-aaatgctgtcttagtgttttcctatttaaaa--gaagtgaatatcactg----------aacat-tttgctgaattt--agGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
| ||| ||| | | | | |||| | | | | ||||| | | ||| || || || | | | ||| | ||||| || |||||||||| ||||||||||| || || |||||||| |||||| ||||| ||||||| ||||| ||||||||||| ||| | ||||| ||| |||| |
gtaggttgtttttagtagacactgtaaaacccttatgctgtgtttgtttgagggagggggagagtaataatgttggttttatgtggatgccttgtacactatactttaattcaaatatttttcttctattttcatcctctaaaccaaacacaacattatagtgtttatgagagcatgtgaactgaaattgcagGACTGGGCAGATCTGTGGCGTCCTGATCTTGCAGGGAGGATCTTGATGGTTGATTCTCCAAGAGAAGTTGTTGGTGCAGTTTTGAAATATATGGGAGCTT
upper sequence: AT1G31410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G17320.1 (Glycine max), 3'ss of exon 1
gttggtatactttgttgttgctaaatgctgtcttagtgttttcctatttaaaagaagtgaatatcactgaacattttgctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
|| ||| | | |||| |||| | | || | | | | | || | || ||| | ||| |||||||||| ||||||||||| ||||| |||||||| ||||| ||||||| ||||||| |||| ||| |||| || ||| | || || ||| | || |
------gtaagttgctttcaataaacactgtaaaactcttgtagtgtgtttatgaga-gtatgtcaactgaaattgc---------agGACTGGGCAGATCTGTGGCGGCCCGATCTTGCAGGGAGGATTTCAATGGTTGATTCTCCCCGAGAAGTTATTGGAGCAGTTTTGAAGTATATGGGGGCTT
upper sequence: AT1G31410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0087g00180.t01 (Vitis vinifera), 3'ss of exon 4
-----------gttggtatactttgttgttgctaaatgctgtcttagtgttttcctatttaaaagaagtgaatatc--actgaacattttgctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
| | | | | |||||| | | | ||| | | || || || | | | | ||| | | || | || | |||||||||| ||| | |||||||| || |||||||| ||||| ||||| | ||||||| |||||||||||||||||||| | || |||||| ||||||
ctcatctcattataaaaacttctagctattgctatggatttttcaaaaactttgttttctataaaaaattattctgggactaagtagtt-gatggttgcagGACTGGGCAGATTTATGGCGACCTGAACTTGCAGGGAGGATTTCAATGATTGATTCTCCACGAGAGGTTGTTGGTGCTGTTTTAAAGTACATGGGAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtgttttcctatttaaaagaagtgaatatcactgaacattttgctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
ttttgct CT-rich tract
ttttcctatttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtatactttgttgttgctaaatgctgtcttagtgttttcctatttaaaagaagtgaatatcactgaacattttgctgaatttagGACTGGGCTGATCTGTGGCGACCCGAGCTTGCAGGAAGGATCGCAATGGTGAATTCTCCTAGAGAGGTTGTTGGTGCTGTTCTCAAATACATGAGAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA