Sequence
atgc intronic sequence ATGC exonic sequence...caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53520.3 |
intron # | 1 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 1
caattattgtgatatttcgtgatgaaatgttt-ccattgggaatgtgtttttctctattgttgatatgatg---attctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
|| | || | | | | ||| || || | ||| ||| | | | | | | ||| | | ||||| | | |||||| || | ||||||||| ||||| ||||| || | |||||||||||||| |||||| || |||| |||||||| |||| || |||||||||||||| ||||||||||| |
catgtttttttgcaacttattatgttattttcactatttacaatataatcatgtgttgcatctgtatattatcaaatctgggt--ttcttaacaat--tattacAAGACCAATGTCATGGGAACCTTGAATATGTTGGGTCTGGCAAAGCGAATTGGTGCAAGGTTCTTGCTAACTAGCACAAGTGAAGTTTATGGAGATCCAC
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 2
--caattattgtgatatttcgtga--tgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
|||| | || ||||| | | | | || | || | | | | | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| |||||| ||||||| ||||||||| || | || |||||||||||||| ||||| ||||| |
atcaatcccctccaatccgtatggattgaaaataaccgaacaagccctaaatgttttgagtttcttttgtctaaaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCAAAGCGAGTTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCAC
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 1
caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC---
|| || | |||| || |||| |||||| | || | | | | | || | | | || | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| ||||| |
-aaggatgtcgccattttttg-cagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacaagACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGCTTG
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
--caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
|| || | |||| || |||| |||||| | || | | | | | || | | | || | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| ||||| |
gggaaggatgtcgccattttttg-cagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 1
------------------caattattgtgatatttcgtgatgaaatgtttc--cattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
| | | ||| |||| | | ||| | | | | || || | ||| || | | |||||| |||||||||| | | ||||||||| ||||| |||||||| || || ||| | || ||||| |||||| ||||||| ||||||||||| || || || ||||| || || || |||||
atatccttcctctctatgttctaactctgactcgccgtgtttttaagttccagctctcttttttcgtaattttttatgttttgtgttg-aattctg--tgatccttaattgttggcttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGAGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGT
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 1
---caattattgtgatatttcg----tgatgaaatgtttccattggg----aatgtgtttttctctattgttgatatgatgattctggt----tgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
|| | ||| || | | | |||| || | ||| | ||| | | || ||| || | || |||||||||| || |||||||||| ||||| |||||||| || || ||| | || ||||| ||| || ||||||| ||||||||||| || || || ||||| || || || ||||| |
atatccttgtctcgatgttctaactctaactcagcgttttttttaagttctaataactcttttttcgtaatttttattttgcgttgagttctgtgatccttaattattagtttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGCGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGC
upper sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC---
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agggtgcca-aatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgatt--acaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164164061|gb|ES117232.1|ES117232EST: CTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATC AAGACAAATGTTAATTGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGA
genomic: CTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatcctttt ... atagttttacAAGACAAATGT-AAT-GGGCACTCTCAATATGTTGGGTCTTGCAAAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
atccttaac putative branch site
atagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC