Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31750.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
gtaagaaaac-atttaactgaaatt-tctcttcttatttgtgcttata-taat--ttgcttaattggaa---ttatacta----aaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
|||| | ||| ||||||| ||| || | ||||| ||| || | || ||| || || || || || | ||| || ||| | ||||| || ||||||||||||||||| |||||||| |||| | | |||||||||||||| ||||||||||| ||||| ||
gtaatttcatgattcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
gtaagaaaac-atttaactgaaatt-tctcttcttatttgtgcttata-taat--ttgcttaattggaa---ttatac----taaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG--------
|||| | ||| ||||||| ||| || | ||||| ||| || | || ||| || || || || || | ||| || ||| | ||||| || ||||||||||||||||| |||||||| |||| | | |||||||||||||| ||||||||||| ||||| ||
gtaatttcatgattcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
---------------------------gtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
|||||| || | | ||| | | ||| | ||||| || ||| || | | |||| ||| |||||| |||| || || ||||||||||| ||||| |||||||| |||| | ||||||||||||||||| ||||| || || || ||
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaattt-----gtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
---------------------------gtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
|||||| ||| || || | | | ||| | | || || |||| ||| | | ||| ||| ||||||||||| || || ||||| ||||| ||||| |||||||| |||| | ||||||| ||||||||||||||| || || || ||
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcag-tacgtgccgttactgttatttgtactgtttgattattcgaaatct-----gtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
-----------gtaagaaaacatttaactgaaatttctctt-cttatttgtgcttatataatttgcttaatt--------ggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
| | | | | | | || | ||| || ||| || | | ||| || ||| | |||| | | |||||| |||||||||||||| |||||||||||||||||||||||||| ||||| | ||||||||||||||||||||||||| || || |||
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
gtaagaaaacatttaactgaaatttctcttctt--atttgt------gcttatataatttgcttaattgga----------attatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
||||| | || | | | ||| | || || |||| | | || | |||| |||| | ||| | | |||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| | ||||||||||||||||||||||||| || || |||
gtaaggttatcttctagttagctttttgttatttgatttattataagattcatcttgtttgtcactatggaaaatctaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
------------------gtaagaaaacatttaactgaaatttc-tcttcttattt------gtgcttatataat-----ttgct-taattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
| | | | | | | || | ||| | | |||| || | |||||||| | || | | || | | |||||| |||||||||||||| |||||||||||||||||||| ||||| ||||| | ||||||||||||||||||||||||| || || |||
gtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
gtaagaaaacatt-taactgaaatttctcttcttatttgt--gcttatataatttgcttaattggaa----------ttatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
||||| | || || | ||| | | | |||| | | | | |||| | ||||| ||| | | |||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| | ||||||||||||||||||||||||| || || |||
gtaaggtcatcttatagttagtttttgttatttgatttatagattcttgttgtttgtctctatggaaattttaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtaagaaaacatttaactgaaatttctct--tcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
| || ||| ||| | || | | | | | ||||| || | | | |||| |||| | | |||||| ||||| ||||| || |||||||||||||||||||||||||| ||||| | |||||||||||||||||||||||||| || || |||
gtaaggacatcaatcgttaggtttttccaagtattaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaat-gattgaaatt-cgtttacagGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
gcttaat putative branch site (score: 4)
ttatataatttgctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT