Sequence
atgc intronic sequence ATGC exonic sequenceTGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttttcgaataaaacataacaactccaattgagctttcaagtacctgtttcatcttatagtatgtatgtaccacaatgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19860.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G432801_T01 (Zea mays), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttt--------tcgaataaaacataaca-actccaattgagctttcaagta--cctgtttcatcttatagta--tgtatgtaccacaatgtag----------------------------------------------------
|| || || || |||||||| || ||||||||||| ||||| || | |||| |||||||||| |||||| ||| || || || ||||| ||| | |||||| ||| || | | || |||||| | | || | | ||| | | | || | | ||| | | | | | |
TGCAGCCGTAATATTGGGCACTGGTACAAATGCAGCATATGTGGAGCATGCAAATGCAATTCCTAAATGGACTGGGTTACTGCCTAAATCTGGAAACATGgttagtgcttgaattcttttatacaaggaataacatagttttatgaaaccatcatatggtcttacgctattagacatccactgtttattcgctggtatggtattcacccacatgagaaacatgtaacattgaaattattcttggtgctctag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G058745_T01 (Zea mays), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttttcgaataaaacataacaactccaattgagctttcaagtacctgtttcatcttatagtatgta---tgtaccacaatgtag--------------------
|| || || || |||||||| || ||||||||||| ||||| || | |||| |||||||||| |||||| ||| || || || ||||| ||| | |||||| ||| || | | | || || | | | || || | ||||| | || || || ||| |
TGCAGCTGTAATATTGGGCACTGGTACAAATGCAGCATATGTGGAGCATGCAAATGCAATTCCTAAATGGACTGGGTTACTGCCTAAATCTGGAAAGATGgttagtgcttgaattctttatactagggatcacatagttgtatgaaaccatcgtatggtcttacaccattagaaccgtgtaaccatgaaatattattcttggtgctctag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G856653_T01 (Zea mays), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttt----tcgaataaaacataacaactccaattgagctttcaag--tacctgtttcatcttatagtatgtatg-taccacaatgtag------
|| || || || |||||||| |||||||||||||| ||||| |||| |||| ||| ||||| |||||| || ||||||| | |||||| | |||||| |||||| || | | | || | ||| | || | | | || ||| | || | || || | | |
TGCTGCTGTAATATTGGGCACTGGCACAAATGCAGCTTATGTGGAACATGCAAATGTGATTCCTAAATGGACCGGGCTGCTACCTAGATCAGGGAACATGgttagtgtttaacttccatcgagtgagtggaattttaatagtctttggaggatgaactagctcaattgatgcgaagtgtggttgtgcggcccaccactca
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G01060.1 (Glycine max), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgt-------ttgtgt---------tttcgaataaaacataacaactccaattgagctttcaagtacctgtt--tcatcttatagtatgtatgtacc-acaatgtag
|| | ||| ||| | || || || ||||||||||| ||||| || |||||||||||||||| |||||||||||| | ||||| ||||||||||| ||||| || | | |||| | | | ||| || | || || | | | | | | || | ||| || | | |||
TGCTGGAGTGATTCTTGGTACTGGGACAAATGCAGCTTATGTAGAGTGTGCACATGCAATTCCAAAATGGCATGGTCTTCTACCAAAATCAGGAGAGATGgtaaacagattatatgacacttattttcttgtgtgatagaactgtgtttataatgattccatgaggcagctaatgggatggtaatgattatttattgattctatag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G12190.1 (Glycine max), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtg----------------ttttcgaataaaacataacaactccaattgagctttcaagtacctgtt--tcatcttatagtatgtatgtacc-acaatgtag
|| | ||| ||| | || || || ||||||||||| ||||| || |||||||||||||||| |||||||| ||| | ||||| ||||||||||| ||||| || ||||| | | | ||| | | || || | | | | | | || | ||| || | || |||
TGCTGGAGTGATTCTTGGTACAGGGACAAATGCAGCTTATGTAGAGTGTGCACATGCAATTCCAAAATGGCAAGGTCTTCTACCAAAATCAGGAGAGATGgtaagtaggttatatggcacttattttcttgtgtgatagaaccgtgtttacaatgattccatgaggcagctaacgagatggtaatgattatttattgattatatag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G35890.1 (Glycine max), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgt-------ttgtgttttcgaataaaacataacaactccaattgagctttcaagtacctgtttcatcttatagtatgtatg-----taccacaatgtag-----
|| || || ||| | || || || ||||||||||| ||||| |||||||||||||| ||||| ||||||||||| | |||| ||||||||||| ||||| || || | || | | | || || | || || | | || | | ||| | | ||| ||| | | |||
TGCTGCTGTGATTCTTGGTACTGGGACAAATGCAGCATATGTAGAACGTGCACATGCTATTCCAAAATGGCATGGCCTTATACCAAAATCAGGAGATATGgtaagtaggttatgaatgcgtgtgagatttagtttcttgtgtgatagattt--gtccttattgtgtgtgatacaaagcatgctgattacttctaagtattatag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G03730.1 (Glycine max), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgt-------ttgtgttttcgaataaaacataacaactc---caattgagctttcaagtacctgtttcatcttatagtatgtatgtacca-caatgtag
|| || || ||| | || || || ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| | |||| ||||||||||| ||||| || || | | | | || ||| || || ||| | || || | || || | || | | | | |||
TGCTGCTGTGATTCTTGGTACTGGGACAAATGCAGCATATGTAGAACGAGCACATGCTATTCCAAAATGGCATGGGCTTATACCAAAATCAGGAGATATGgtaagtaggttatgaatatgtgtgagacttaatttcttgtgtgatagagttatccttattgtgatacaaagcatgctgattacttctaaatattatag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G01070.1 (Glycine max), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttttcgaataaaacataacaactcc-------aattgagctttc---aagtacctgtttcatcttatagt-atgtatgtaccacaatgtag----------------------
|| | ||| ||| | || || || ||||||||||| ||||| || |||||||||||||||| |||||||||||| | | ||| |||||| |||| | ||| | || | | | | | | || || | || | | | | || | | || | | | ||| ||| | |
TGCTGGAGTGATTGTTGGTACTGGAACAAATGCAGCTTATGTAGAGAGTGCACATGCAATTCCAAAATGGCATGGTCTTCGACCAAAATCAAGAGAGACGgtaagcaggttatatgacactttttttattgtgtgatagaactgtgtttaccatgattccatgaagaaggtaatgattagctgtgtgccaaagcttgctgattatttattgattctatag
upper sequence: AT2G19860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 5'ss of exon 5
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgt-gttttcgaataaaacataacaactccaattgagctttcaagtacctgtttcatcttatagtatgtatgtaccacaatgtag-----------------------------------------------------------------------------------------------------------------
|| ||||| || ||||| || || ||||||||||||||||| ||||| ||||| |||||||||| ||||||||| | ||||| ||||| ||||| |||||| | ||| || |||| | | | | || | | || | | | |||||| || || | | | ||
TGCTGCAGTGATCTTGGGTACTGGAACAAATGCAGCCTATGTAGAACGGGCACAGTCAATTCCCAAGTGGCATGGTCTCCTACCGAAATCTGGAGATATGgttagcagttctcttataatttccatctattgatat-gtgattaggaatgtactatccatcttctattaaaaacaaaaaatcttgacttttttttaatgtctctttcctgatatagaaatgtttctgtggtttggaacctagtatacaagttatgctattatgtcggaagataaataattttcttaataaaatttctgtagMapped 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|125093727|gb|EL151266.1|EL151266EST: CACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATG GTGNTCAACATGGAATGGGGAAACTTCAGGTCAT
genomic: CACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttt ... cacaatgtagGTGATCAACATGGAATGGGGAAACTTCAGGTCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTCGCAGTTATTTTGGGCACCGGCACAAATGCAGCCTATGTCGAACGTGCACATGCAATTCCCAAATGGCATGGTTTGCTACCCAAATCAGGAGAAATGgtttgtgttttcgaataaaacataacaactccaattgagctttcaagtacctgtttcatcttatagtatgtatgtaccacaatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA