Sequence
atgc intronic sequence ATGC exonic sequencegtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G02460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatc----tgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|| | | | | | | | ||| || | || || | | | | ||| || | ||| ||||||| ||||| ||| |||| || ||| | ||||| |||||||| ||||||||||| || |||||||||||||| || || || |||||||||||||| ||||
gtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
gtctatcctctagatatttcccttgtttcccattttt---ctttcttttagtatggga--ctaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|| | | | | ||| ||| || | | | | | || | ||| || | | || | ||||||| ||||| ||| |||| || || ||||||| |||||||| || || ||||| |||||||||||||| || || || || |||||||| ||||| ||||
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcat-tttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
| | || | | |||| | | | | ||||| | ||| ||| || ||| ||| | || ||||||||||||||| |||| || | |||||||| ||||||||||| || ||||| || ||||| || || ||||| || |||||||| |||||||||||||
--gttttactcaggaacccatcacctttc---tgtgcttgttacaaagtatttca-taatattgatcattttaaaa-ctacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
| || | | || | | || || | ||||| | ||| ||| | ||| ||| | || ||||| ||||| ||| |||| || | |||||||| |||||||| || || ||||| || ||||| || || ||||| || |||||||| |||||||||||||
---gttttactcaggaccccatcaccttgctgtgcttgttacaa--agtatttca-taatattgaccattttaaaa-ctccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatc---tgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|| | | ||| || | | | |||| || | || | | | | || | | | | ||||||| ||||| ||| |||| || || ||||||| |||||||| ||||||||||| |||||||| | ||||||||||||||||||||||||||||||||||
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAAMapped 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|124933181|gb|EL010365.1|EL010365EST: TTTATGACAGAGATGTCGGATATGTTCAG GGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGAT
genomic: TTTATGACAGAGATGTCGGATATGTTCAGgtctatcctc ... atatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
ttctaat putative branch site (score: 2)
ttttctttctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT