Sequence
atgc intronic sequence ATGC exonic sequenceGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21160.3 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G161728_T03 (Zea mays), 5'ss of exon 1
------------------------GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgt---gactctttgcttctctttctagttttggtttatctt-tggtgaaaatttgccattggattcc---attaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagtttt-caactttccag---
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CTATTTGTTTTTTGTGCATTTCAGATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgtattgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatg-atctttagtctgtcatagttcatgctta--gactcctt----actcatttcatggttccgctattctccatcag
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G161728_T04 (Zea mays), 5'ss of exon 4
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgt---gactctttgcttctctttctagttttggtttatctt-tggtgaaaatttgccattggattcc---attaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagtttt-caactttccag---
|| |||||||||||||||||| | |||||||||||| | | ||| || || ||||| | | |||||||||||| | || ||||| ||| || || | | || | || || || || | | | | | || | || | || || || | | ||| | | | |||| | || | | || || ||| | | | ||||
ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgtattgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatg-atctttagtctgtcatagttcatgctta---gactccttactcat---ttcatggttccgctattctccatcag
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G13700.1 (Glycine max), 5'ss of exon 4
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtga--aaatttgccattggattccattaa-gatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
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GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAGgtaa--accattcacatgtaccaccattcataggttgtctattgttatggaaggcatttctgccttggatcaaagacttattttccctctaattgtaaaata------------------------------------------------------------------
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G02830.1 (Glycine max), 5'ss of exon 4
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttg-tgactctttgcttctctttctagttttggtt-tatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
||| || || |||||||| |||||||||||||||||||| ||||| |||||||||||||| | |||||| |||||||| | || | | || ||| | | | | | || | || | ||| || | | | || || ||||| | | | ||||| |
GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAGgtaaaccattcataggttgtctcattgttatggaatgcatttctgcccggatcaaagaattatttttcctctaattg---ta-aaatattttatttgatttaat---------------------------------------------------------------
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 5'ss of exon 2
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
|||||| ||||||||||| ||| |||||||||||||||||||||| |||||||| |||||| ||| || |||||||| | || | | | ||| ||||| | ||| |||| | | | | ||| | || | ||| || || ||| | || |
GTCAGCCAATATTGGAGTTTTTGTATGCTTAAAATGTTGTGGTGTGCACAGAAGTCTTGGCTCTCAAATATCAAAGgtaactattcctaa-tccacttaagagtttaga----------aagaagattttc------actttactaataaggaatttaaactgagttccttcttcgtttgtctacaacaaatt------------------------------------------------
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 5'ss of exon 2
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
|||||| ||||||||||| || ||||||||||||| |||||||| |||||||| |||||| ||| || |||||||| | || | || ||| | ||||| ||| |||| | | | | ||| | || | ||| || || | || | || |
GTCAGCCAATATTGGAGTTTTCGTATGCTTAAAATGCTGTGGTGTGCACAGAAGTCTTGGCTCTCAGATATCAAAGgtaactattcctgatccactttactaaat--agtttaga---aaagaagattttc------actttactaataaggaatttaaactgagttcc---ttcttcatttgtctagaa---------------------------------------------------
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 5'ss of exon 4
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
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GTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAGgtagctgccctat-tattgcttcgtatttagttatcatcatgcatcatagtgtat--gtgttttcttttttatctttttattttttat-ttttgtactggaaat-------------------------------------------------------------Mapped 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|125090685|gb|EL148577.1|EL148577EST: CTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGACAGTCATATCTCAAAG GTCTTATCCGT
genomic: CTTAAAATGTTGTGGTGTCCACAGAAGCCTTGG-CAGTCATATCTCAAAGgttgtgactc ... aactttccagGTCTTATCCGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccag
- - - - - - - - - - - - - - - - - - - - - - - - AGAAGC