Sequence
atgc intronic sequence ATGC exonic sequencegtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55930.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 12
gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
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--cttatattaagcatagttttcttaagtggaatgtgctactgcaatcaccatatgctggatatgaggttcacttggaatttggaa-atgcatttgttt--------gcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 6
gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattg-cttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
||| | || | || || | |||| || | | | | | |||||| ||| | ||| | ||| ||| ||| |||||| |||||||||||||| || || ||||||||||||| | ||||| ||||| ||| | ||||| || || || ||||||||||| | |
----tattccct-tggcagtcatcattatgtggtgctgtgtatttctgtcattttttcatagattggcttatatcttgag---acacttggacaccattt----ttttgcagGGACATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGCATCTTTTGGCTATATTCCAGAAGAAGGTGGGAAAATGCTTGTGATTCTTGAAAAGAATTTCA
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 12
gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatccttttgtttcccttt--tcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
| | | || | | | | || || | | | || || || || || | || | |||||| |||||||| || | ||||| ||||| ||||||||||| ||||||||| ||||||||| |||||||||||||||| ||| |||||||| | | ||| || |||||||| || |
-tcttgcaagttgcaagggaaagtgaatggtatcatgcca--------atccagtcccta---ttaattctcaaatatacattca-tatcctcttgtttcctgttggttacagGGTCATCAATATGAGACAGTATCAGGTTTTATCTGTGAGGTATTTGGGTATATCCCAAGGACTGGTGAGAGCATAAAGGTGGTACTTGAAAATCAAGAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 14
--------------------------------------------------------gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatcctttt------------gtttcccttttcgcagGGC---CATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
| || ||| || | | ||| | | || | | | | || ||| | | || ||||| | | | | | | | |||||| || | |||||||| || ||||||||||| |||||||||||||| || || || || || |||||| | | ||| ||||
gtaggctactgatgaaagggcttagaatctggtgacaaatgttgggatagaagctgatcatctacacttttattggcgaagtagcgaaccattcggaactagacctttggttcctagttttgagaagta-taccatacaaactgtggtcgttgaaatctaacaatgtgatctgtagcagGGTTCACACCGCTATGAGACTGTATCAGGTTTTGTATGTGAGGCCTTTGGCTACATTCCTCGCACTGGAGAGAGTACCAAAATTACACTTTGGAAGGCGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaagattgcttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
ctatccttttgtttcc CT-rich tract
tataaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA