Sequence
atgc intronic sequence ATGC exonic sequencegtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02840.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattgga-atttgcttcgaaattttgag--atttctctttgttttcatgctcttcgatgtttgatttcgtatctggatt---ttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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--------gtaagccagcatccccctgtttctcccctttccccctccattcgtttcagtctgctgattcgtttggtgcaattttcgcccgaatcggtgcggattttggcgcgggaattgcgcttttacagGTTCTTGATGAAGCTGAACAACGAAACGGTGACCATCGAGCTTAAGAACGGCACCGTCGTACACGGAACCATTACCG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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---------------------gtctcacatcttcattctcattccgcgtttccct----ttttctcactttttttttttttcaa----tttgaagctaaaatgtgtat---aaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 2
------------gtatggtttctactcggattctctttatttcttcggtttaattgg--aatttgcttcgaaattttgagatttctctttgttttcatgctct----tcgatgtttgatttcgtatctggattttttc-gcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG-
||| | ||| | | || | ||| ||| | | || | || || || | | | | | || |||| || ||| || | || | || || | | | |||||||||| ||||| |||||||| ||||| || ||||| ||||| ||||| || || ||||||||||| |||||||| |
tttttctctgctctatc-tctctctttgtttttttttttttttgttgcgttggtaaattgatctgtttatgtgctgctatgtattttattttttttattttctgggatcaaagtctaataatatacgaacactgcatgagcaggTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattgga--atttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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---------------------gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtct---aaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
gtatggtttctactcggattctctttatttct-tcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggatt-ttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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----------------gtttttctctttctttgttgcgttatctgttaattgcgt-----tttt---atttttttttcattttctgagat-caaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttt--tcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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----------------------------------------------gtctgctt---atttttcagtttttctcttgttttcattctcattaactattgttgacctagcttgatacgaaatttcagGTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtttctactcggattctctttatttcttcggtttaat-tggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatt-tcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
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-----------------------------------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S90_45V6.1 (Physcomitrella patens), 3'ss of exon 1
-----gtatggtttc-tactcggattctctt-tatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttc--gtatctggattttttcg-------cagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
|| || | | || | ||| || | | | | ||||| || | | || ||| | || | || || |||| || | ||||| | || || || | | ||| |||||||||||| ||||||| ||||| |||||||| ||||| || || || |||||||| || || || || || |
gtgcagtgcctttcccttcttttactctgttgtgtatttcgggtttcgtttaggatagtttttccttttctggtttgtgatgtggattattgctgttggcgtgacgatttttgggatttgtgggttgttggtgggtccagATTTTTGATGAAACTGAACAATGAAACGGTTTCAATGGAGCTGAAAAATGGTACCATTGTGCACGGCACTATCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
gtttgat putative branch site (score: 5)
ttttttcgc putative PPT
atttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA