Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23940.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 10
-------------------------gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
| ||| | | | | | | || || ||| | || | ||| || ||| | ||||| | || || || || ||||||| || || ||||| || ||||| |||||||| ||| |||| || || ||||||||||||||||| |||||||| |
tatttccttttacgctcttgacaagggaatgcattagttcactgggacaaccatgcatagtcttgttctgaattact---ctgctggcatgcaat-cacaacagGGGAAGGTAGTAGTGATACGAGGAGAAGGACCGAAAGGTGGACCAGGGATGCCTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------------------------------------gtaatttcctttctgata-tgaagt---tcatctcaggagctggttatatatctt---ttatctgatgaaatgtatcgtgttt-cagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
| | | || |||| | || | | | |||| || | ||| | || | || || || | ||||||| || || || ||| ||||||| || || |||||||| ||||| |||||||| |||||||| || |||||||||||||||||||| ||||| ||||
gtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgcattcgtatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 10
--------------------------------------------------------------------------------gtaatttcctttctgata-tgaagttcatc--tcaggagctggttatatatcttttatctgatgaaatgtatcgt-------gtttc---agGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
| | | || ||||||| || | | || | |||| ||| | || || | | | ||| | ||||| |||||| || || || ||| ||||||| || || ||||| || ||||| ||||| || |||||||| || ||||| |||||||||||||| ||||||||||
gtaatatgtgcagtgcaagtattttctgcatttgctactgccgctattgaatgccatttcttcctttttttgtagattgccttttcttctctctgatagtggaatatattgtttcagagcaagttttgcattcttatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
-------------gtaatt-tcctttctgatatgaagttcatctcaggagctggt--------tatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
||| || | | ||| | | | | | ||| || || | | | || | | ||| || | | | | |||||||| | |||||||| ||||| |||||||| || || || ||||| || |||||||||||||| ||||| |||||||||||||||||||| ||||||||||
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattt-tttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
----------------gtaatttcctttctgatatga--------agttcatct-caggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
|| | || |||||| || | || || | || ||| || |||| || | | || |||||||| | || ||| |||| ||||||||||| || || || || ||||| |||||||| |||||||| || ||||| ||||||||||| || |||||||| |
tcatattttttctattttatgtgtctcactgataggatggtgtataattgattcatcaaaatgggatatctaattttttgcttttctgttatac----tttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36479 (Selaginella moellendorffii), 3'ss of exon 9
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
| | | || ||| | |||| | | ||| ||| || | | ||||| | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| || | || |
-------------------gttctctctgtccaaagcaag--atatgataatca-ctggtgattggtgaaatact-cagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ18570 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA--
| | |||| | | | | || || || || || | || | | ||| | ||||||| |||||| | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| || | || |
---gtatacttttttctct-atgtccaaaacaagatatgataat-cactggtgatc-ggtgaaatgc--------tcagggctccgtgattgttatcagGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGAAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ18571 (Selaginella moellendorffii), 3'ss of exon 11
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
||| |||| | | | || || || || || | || | | ||| | |||||| |||||| | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| || | || |
---gtttacttttttctctct-gtccaaagcaagatatgataat-cactggtgatc-ggtgaaatac--------tcagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36478 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
| | |||| | | | || || || || || | || | | ||| | |||||| |||||| | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| || | || |
---gtatacttttttctctct-gtccaaagcaagatatgataat-cactggtgatc-ggtgaaatac--------tcagGGCGCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGAMapped 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|125159717|gb|EL187667.1|EL187667EST: GAGAGGAATCTATGTTGGCTGCTATATCAGCAGACCCAATGAGTTTTAAG GGAACTGTGGTTGTTA
genomic: GAGAGGAATCTATGTTGGCTGCTATATCAGCAGACCCAATGAGTTTTAAGgtaatttcct ... cgtgtttcagGGAACTGTGGTTGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
atctgat putative branch site (score: 4)
ttatatatcttttatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG