Sequence
atgc intronic sequence ATGC exonic sequenceATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagatccttacattgaccctctcacatttcttgatgatgaattgactaaaaatatgtttctttcttgtttgaatgaag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14040.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACC------------AGGCTTAATgtaag-atccttacattgacc------ctctcacatttcttgatgatgaattg---actaaaa--atatgtttctttcttgtttgaatgaag
|| | || |||||||| || ||| |||| |||||| ||||||| ||||||||||||||| | || ||| | |||| | | | | || || ||||||| || ||| || || ||| || | |||||| | || | ||| | || || || ||| || || ||
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaaattgctccaatgtctgt-tgcag
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM5G837351_T01 (Zea mays), 5'ss of exon 2
---ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTG-ATGCTTCT-GCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagat-ccttacattgacc----ctctcacatttcttg--atgatgaattgactaaaaatatgtttctttcttgtttgaatgaag
| | | |||| | || || || || | | | | | || || | | |||| || || ||| | || | | | || || | ||| || ||||| ||| ||| | | | || |
GCACTGGAATTAACAAGCTGGATTACCTTGCAACGATGGATTTGGACCCCGACTCTCCTACATACTCCCAGgtgatccacaggctctcagtcacccacatcggcgatgagctgcatcactctggctggaactcgtgcagctcttgccatggtga-tccatcagcaaagcatc--------------------
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G058930_T01 (Zea mays), 5'ss of exon 5
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagatc------------cttacattgaccctctcacatttcttga-tgatgaatt---gactaaaaatatgtt-----tctttcttgtttgaatgaag
| || || |||||||| || ||| |||| |||||||| |||||||| |||||||||||| | || || | | || | ||| || |||| || ||| || | | | ||| | | || | | || ||| | |||| | ||||||| ||| || || || ||
ACATCGGCGATGAGCTGCATCACTCTGGCTGGAACTCGTGCAGCTCCTGCCATGGTGATCCATCAGCAAAGCGTCGCTTCCTGATCCTACCTTCGTTGCTgtgagtacagaataagtggacatggtctgaatcaattgaatgaatcggctgctgacctcaggactgagaatatgtggtgtggcttcaatggttatttgcag
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G117726_T01 (Zea mays), 5'ss of exon 1
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaag--------atccttacat----tgaccctctcacatttcttga-tgatgaatt---gactaaaaatatgtt-----tctttcttgtttgaatgaag
| || || |||||||| || ||| |||| |||||||| |||||||| |||||||||||| | || || | | | | ||| || | || || ||| || | |||| ||| | | || | | || ||| | |||| | ||||||| ||| || || || ||
ACATCGGCGATGAGCTGCATCACTCTGGCTGGAACTCGTGCAGCTCCTGCCATGGTGATCCATCAGCAAAGCGTCACTTCCTGATCCTTCCTTCATTGTTgtgagtatagaataagtggacatggtctgaatcaattgaatgaatcggctgctgacctcaggactgagaatatgtggtgtggcttcaatggttatttgcag
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 2
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaag--atccttacattgaccctct-----cacatttcttgatgatgaattgactaaaaat---atgtttcttt-cttgtttgaatgaag---------
|| |||| || || | || |||||||||||||| || ||||||||||||||||| || | || || || |||| | || || ||| | | ||| | |||||||| | | || | | ||| | | | || | | | ||| | | | | ||| | | ||||
ATTTAGGTGACGAATTGCATCACACTGGTTGGAATTCATGCAGCTCTTGCCATGGAGACCCCTCGGCAGACCGACGATTTCTCATCGCACCTGCACTCGTgtgtgtaatccttaccctccctttccaactatataaatctaaaaggacatttcattcataattacaaatatatcaacttatgaaactgaaaaacatggaa
upper sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 2
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagatcc-----ttacattgaccctc---tcacatttcttgatgatg-aattgactaaaaata-tgtttctttcttgtttgaatgaag----------
|| |||| ||||| || |||||| |||| |||||||| ||||||||||||||||||||| | || || | |||| |||||| |||| ||| ||||||| | ||| ||| |||| | || | || | | || |||| | | | | | ||| || ||
ATTTAGGGGATGAACTACACCACTCTGGGTGGAACTCCTGCAGCTCTTGCCATGGTGATTCATCACAAGAACGGCGTTTTCTTGTCCTACCTTCCTTGGTgtaagaactggaatttatgttgcattagggactacatattttaagcttgtagcagtttagtaataatactggtatgaagaatgagtgcagagtctaacttMapped 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|124973240|gb|EL046886.1|EL046886EST: TGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAAT TTCTGGTCGCATCTATGCAATCGACACAAAGACCGACCCAAAGGCTCCGTC
genomic: TGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagatcct ... ttgaatgaagTTCTGGTCGCATCTATGCAATCGACACAAAGACCGACCCAAAGGCTCCGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACCAGGCTTAATgtaagatccttacattgaccctctcacatttcttgatgatgaattgactaaaaatatgtttctttcttgtttgaatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT