Sequence
atgc intronic sequence ATGC exonic sequencegtactatttcatatctctctctctcgtgtcttttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 1
---------gtac-tatttcatatctctctctctcgtgtcttttctgatgatttcctcct--gctatttgacttttcctcctgcta--tctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
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aacatataaatccatctttcaattgcatatctatttttgcttgtgcaatgattgccatgtaagcatttcaatacacactaaaggaagggttgttgtgcagGTTTCTTTGTCACAATTTGGATTGCTGCTGTAATGTTCAAGTCAAATGATATATTGCGGAAGCAAACTGCTTTGAAG
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 1
---gtactatttcatatctctctctctcgtgtcttttctg----atgatttcctcctgctatttgacttttc-ctcctg------ctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
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ttctaactaagttattatcctgtcaatcactctttttttggagcaaaggttgttgggagtgcctgagtgtccactaatggaaggattgttttgtgtgcagGTTTCTTTGTCACAATTTGGATTGCTGCGGTAATGTTCAAGTCGAACGATATATTGAGGAAGCAAACTGCCTTGAAG
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G890843_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------gtactatttcatatctctctctctcgtgtcttttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
||||||| | | | || | | || | | |||| || ||| | || || | | | | |||| |||||||| | |||||||||||||| || ||||||||||| |||||||| || ||||| || ||| |||||
gtggtgctctcatttcccttgtcaacagagcgcaaattcatatgtacatgaccaacttgatgcttagaacctagggtcacactattt-gcaaattgaagtaatgtagatgtgtgagggaatgcag---gctaattttcttcttcttttgaattgttttgcacagGTTTCTTTGTGACAATTTGGATTGCTGCGGTGATGTTCAAGTCCAATGATATCCTGCGTAAGCAGACTGCTCTGAAG
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
------gtactatttcatatctctctctctcgtgtcttttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
| || || ||| | | | ||| | || || |||| | | ||||||| || | ||| | | ||||||| ||||| ||||||||||||||||||| | |||||||| ||||||||||| | ||| ||||| || ||||||
ggtgcgctcttagtttttatgttttgagttactgttctatccgagaatttatttat-ttatttgatgttgttg---ggtattgcaatg-caGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
tttgacttttcctcct CT-rich tract
atgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactatttcatatctctctctctcgtgtcttttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG