Sequence
atgc intronic sequence ATGC exonic sequence...gtgcggtttcattttcgctttaatattgttagccaatgcggcaatgcgtctagtttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01060.3 (Glycine max), 3'ss of exon 1
-gtgcggtttcattttcgctttaatattgttagccaatgcggcaatgcgtctag---tttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
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attgatgaaaaacaagtggataaatattgtca--tgagtttgtaattcttgaatgctttttccttttttggctcattctttactttgttccgttgttt--atagGGATGAGAAAGGACTCTTTTATGCATTAGACCTTGGTGGCACAAACTTCCGAACCCTTCGCGTGCATTTAGGTGGGAAGGAGAAAGGTGTTGTCAAAATA
upper sequence: AT4G29130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G12190.1 (Glycine max), 3'ss of exon 1
--------gtgcggtttcattttcgctttaatattgttagccaatgcggcaatgcgtctagtttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
| || | || || | | |||| | ||| | | |||| ||| || | | || | | | || | |||| | | |||||||| || || |||||||||||||| ||||| || || ||||||||||| | | || |||| | | || |||||| | | ||||||| ||| |
tgaaaagcaagtggataaatattt-ttgtcatatgaatttgtaattctggaatgtttcttcctt-----tcttggctcattctttactttgtttcattgttt--atagGGATGAGAAAGGACTCTTTTATGCATTAGACCTTGGTGGCACAAACTTCCGAACCCTTCGAGTGCATTTAGGTGGGAAGGAGAAAGGTGTTGTCAAAATA
upper sequence: AT4G29130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 1
gtgcggtttcattttcgctttaatattgttagccaatgcggcaatgcgtctagtttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
|| | | | | | | | || | || | || | | |||| | || || | | |||||||| |||||| | ||||||||||||||||| || || ||||||||||||||| ||||||||| | || ||||| | |||||||||||||||||
acctggaaatggacaatttcagttgtccagatctgttacactgattaagagatatttcagctgaacatgccacttattctccctctttttttttttttagGGATGAGAAGGGTTTGTTTTATGCATTGGACCTTGGTGGCACAAACTTCCGTGTCTTGCGTGTGCAATTGGGTGGGAAAGACAAGCGTGTTGTTAAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgtctagtttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
cattaat putative branch site (score: 3)
taccattaatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcggtttcattttcgctttaatattgttagccaatgcggcaatgcgtctagtttcatgttgtaggtctgtcttacatttactaccattaatataacagGGATGAAAAGGGTCTCTTTTATGCATTGGACCTAGGGGGGACAAACTTCCGTGTCATGCGTGTGCTTCTTGGCGGGAAGCAAGAGCGTGTTGTTAAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - ccaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actacca