Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35210.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcg---tcgatcagatctg-acagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
|| || || || || ||| | | | | | || | || | | | | || | ||| | | | | ||||||| || || |||||||| || |||||||| || ||||| ||||| || ||||| |||| ||||||||||| ||||| || | || || || || ||||
gtactgtggattagattggattttatgggtgatcgatttgattgtggagtcgggattgatc-gcactttcttttgctctgtgtgagtgccgcctgtgcaatattttttgtgtgtgtgcgaattccgtttctgatggcggtgcaagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
upper sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------------gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
|| ||| || | ||| |||| | || | | | || | ||| | | | || | || | |||||| ||||| ||||| |||||||||||||||||||| || ||||| ||||| || || |||||||||||||||||||||||||| || || || || ||||| ||||
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtt-tgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
upper sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------gtaatgttaacgatgt-tctacag-----aatctat-agattcgatta-agatct-cgaagttcgtcg-atcagatctgaca---gatttaggatttatctttgaatatttt--ttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
|| | | ||| | | | | || || |||| | || |||||| || ||| | | | ||| || || | || | ||| | |||| || ||||| ||||| |||||||||||||||||||| || ||||| ||||| || || |||||||| ||||||||||||||||| || ||||| || ||||| ||||
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttttgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG
upper sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
| || || | | ||| |||| | || |||||| || ||| |||| ||||| | | ||| ||| | | | | ||||| |||| ||||||||||| |||||||||||||| || ||||| ||||| || || |||||||| ||||||||||| ||||| || || ||| |||||||||| |
gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattggatct--cggttttttattttgtttctttttggttttt--agATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGMapped 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|19877026|gb|AU237857.1|AU237857EST: ATGACAAGATCTCTGTTTTTAAGAAACTCAAAGCCAAATCAGATAATAAG ATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTAC
genomic: ATGACAAGATCTCTGTTTTTAAGAAACTCAAAGCCAAATCAGATAATAAGgtaatgttaa ... ttttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
atctgac putative branch site (score: 3)
tatttttt putative PPT
atttaggatttatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT