Sequence
atgc intronic sequence ATGC exonic sequencegtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gtcagcatttc--aatcagggtggagaag-ttgaattaccatcttcatttccaattcatgatgctattgagatt-tactactgatcta-ttttgttttttgc------cagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
|| ||| ||| || | || || | | ||||| || || || | |||| | || | ||||||| || |||||| ||| ||| | | ||||| ||||| || || || || || || ||||||||||||||||||||||| |||||||| | || || |||||||||||||| ||||||
gttagtttttatttgctatttccatctcttgctattttgaacaaaacatgaaattcatatccttttttgtaaatgtttgttctgtagctttattcaccattgacaaagaacatacaataacatattcatataattctactgaagtaaccttgtttcttgtgtgctacagGTGTTCTTTAAGGATGTAGCTGGCTGTGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------gtcagc-atttcaatcagggtggagaagttg-aattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttg-ccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
|| || | ||| | | | | | | ||| | | | | | | | | || | | | || ||| ||| | || | |||| | | |||||| ||||| || || || || || ||||| |||||||| ||||| ||||||||||||||| |||| || ||||| |||||||| || ||||
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttg---ttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
--gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttg-ccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
|| |||| | | || | | | ||||| | | || | | || |||| ||| | | | |||| | | |||||| ||||| || || || || || || ||||||||||| ||||| ||||||||||||||| | ||||| ||||| ||||||||||||||||
ttgttgtagcttcatttgcccttttcttaagaaacaaagcatactacatgaaattcgaagatttgtctt--ttcatcaatg-tctacttttctgctggtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
| || || || || | | || | | | ||| | | ||||| | ||||| || || | | ||| |||| ||||| ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||||||| | || |
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctgg-taaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgc-cagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
| | || || || | | || | | | ||| | | ||||| | ||||| || || | | | || ||||| ||| | ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||||||| | || |
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgc-taaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
| || || || || | | || | | | ||| | | ||||| | ||||| || || | | ||| |||| ||||| ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||||| ||| |||||||||||||||||| | || |
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctgg-taaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATG----CGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG---------------
| | | || ||| | | | | | |||| | ||| | | | || | || || ||| | || ||| |||| ||||||| || ||||| || || || || ||||| || |||||||| ||||| |||||||| ||||| |||| |||||||||||||| || |||||||
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcag--caaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------------------gtcagcatt--tcaatcagggtggaga--agttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctatttt--gttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
|| | || ||| | ||| | | | || || | ||| | ||| | | ||| ||| | | ||||||||| | | ||| | | ||| ||||||||||| ||||| || || || || |||||||| ||||||||||| || ||||| |||| || || ||||||||||| |||||||
gttagctaactgtttcttttgtcaaaggtggtttgtctttagtttgcagcatccaatatttttacagtatacaataattattatatcctccttgctcacctatggttataatcattcgattttctctctctgactattattattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG
upper sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
| | | | | | | || |||| | ||| |||| | | | |||| || ||| | || ||||||||||| || ||||| ||||| |||||||| || ||||||||||| || ||| | |||| || ||||||||| |||| | || |
-----------------------------gtgatgtc-ttatgactcccggaaaatgacg-----gagctttattt----tgtgcgttgtgttgctgcagGTGATGTTCAAAGATGTTGCTGGTTGCGACGAGGCAAAACAAGAGATCATGGAATTTGTTCACTTCTTGAAGAATCCCAAGAAATATCAAGAACTTGGGGMapped 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|164000219|gb|ES018778.1|ES018778EST: TAACGAGAGCAGATAAAAACTCCAAGAATAAG ATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAA
genomic: TAACGAGAGCAGATAAAAACTCCAAGAATAAGgtcagcattt ... tttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
tactgat putative branch site (score: 2)
tctattttgtttttt CT-rich tract
atctattttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA