Sequence
atgc intronic sequence ATGC exonic sequencegtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04040.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G035421_T01 (Zea mays), 3'ss of exon 3
----------------gtttttatccaaaacccgaaatcttgaattttctttgattggtatcaga--gattttagacttgcctgagattcttattgggt--tgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
|| | | | | || | ||| | ||| || || ||| | ||| | | | ||| | | | | | |||| || ||||| |||||||| ||| || ||| ||||||||||| || || || ||||| || |||||||||||||| ||| | |||||||| | |||
gtgtgcaatgtttcttattctctctccttgcatgcaactgttcttttcacattatttaaataaggtcaattattgacacagtaaacttacacattatatctttcccactatcatcagTATTCCAAGATGATACAAAACCCGTCTTATGCTGAGCTTCAGAAGGCTGCGAATCAAGGTAGGAGATGCACTTGGGAAAAGTTATCAGCCATCAGGGCAA
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G34500.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------gtttttatccaaaac-----ccgaaatcttgaattt-----tctttgattggta-----tcaga-gattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
|| ||||| |||| | ||| | |||| || | ||||| |||| || | || | | || | | |||| || | | |||||| || || ||||| || || || |||| |||||||| || || ||||||||||| ||||||||||| ||||||||||| || ||||||||| |||
gtatgtgcccaagaacaattaaatactacgttttatttgaagataaaagaaataactagtgtttattaaaaatgggtttaggaatttattatttatatatcatatattggggaagattcagttgaatagtgattaacttgtgtatgttatctttccctgatcctgctccagTACTTAAAAATCATACAGAACCCTTCTTATGTAGAGCTTCAAAAGGCAGCTAACCAAGGGAGAAGATGCACCTGGGAGAAGCTTTCGGCCATAAAAGCAA
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G16440.1 (Glycine max), 3'ss of exon 1
---gtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgt---agTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
||||| | | ||| | ||| |||| | | || | ||||| | | | | || || | || |||||| || || ||||| || || || |||| |||||||| || || ||||||||||| ||||||||||| ||||||||||| || ||||| ||| |||
tagaaatttatt---atttttatatcatttattggggacgattcaattgaatagttattaacttgtgtatgttgtctttttttccctgatcctcctgctccagTACTTAAAAATCATACAGAACCCTTCTTATGTAGAGCTTCAAAAGGCAGCTAACCAAGGCAGAAGATGCACCTGGGAGAAGCTTTCGGCCATGAAAGCAA
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G28660.1 (Glycine max), 3'ss of exon 2
----gtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
| ||||| | || | | | | | || | || | | || || | || || | | | ||||| | || |||||||| || || || ||| |||||||| || || || |||||||| |||||||| || |||||||| || |||||||||||| |||
tcaggagtttatttgtgtatcatttactaaagatgattcagttaattaatgattaaattgtgcatat-tgtgactgttgttttacctgtgtcctgttccagTACACCAAAATTATACAGAACCCTTCTTATGGAGAGCTTCAAAAGGCAGCCAACCAAGGGAGAAGATGTACCTGGGAGAAACTTTCAGCCATAAAAGCAA
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G31410.1 (Glycine max), 3'ss of exon 2
----gtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
| ||||| | | | | | || | | || | || | | || || | || || | | | ||||| | || |||||||| || || || ||| |||||||| || || | |||||||| |||||||| || |||||||| || |||||||||||| |||
tcaggaatttatttatgtatcatttacgaaagatgactcagttaattagtgattaacttgtgcatat-tgtgactgttgttttacctatgtcctgttccagTACACCAAAATTATACAGAACCCTTCTTATGGAGAGCTTCAAAAGGCAACCAACCAAGGGAGAAGATGTACCTGGGAGAAACTTTCAGCCATAAAAGCAA
upper sequence: AT5G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g05800.t01 (Vitis vinifera), 3'ss of exon 2
-----gtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
|| || | || ||| | || | | | | | | ||| | | | | ||| | |||| ||||||| || ||| ||||||| || || || | |||||||| || || || ||||||||||| || ||||||||||||||||| |||||||| ||| | |
ttttttccttcatggggcagtggattaattggcatcatctttctcactgttactaactagctgtttgtttttccaaccttctttgttttccctttta--cagTACTCAAAAATTTTACAAAACCCTTCTTATTTGGAGCTTCAAAAGGCAGCCAACCAAGGAAGGAGGTGCACTTGGGAGAAGCTTTCAGCCATTAAAGCCAMapped 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|124956636|gb|EL031540.1|EL031540EST: TGCCTGCTACTCTTGCTCAG TACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCT
genomic: TGCCTGCTACTCTTGCTCAGgtttttatcc ... ttttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCT
EST:
gi|152033763|gb|BP815399.2|BP815399EST: GGAGTGGGAAGGTGATGTTACAGTTGTAATGCCTGCCTACTCTTGCTCAG TACTCGAAGATTATACAAAATC-GACTCATGTCGAGCTTCAGAAAGGGGCT
genomic: GGAGTGGGAAGGTGATGTTACAGTTGTAATGCCTGC-TACTCTTGCTCAGgtttttatcc ... ttttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
attcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatccaaaacccgaaatcttgaattttctttgattggtatcagagattttagacttgcctgagattcttattgggttgtggattttgtgtagTACTCGAAGATTATACAAAATCCGACTCATGTCGAGCTTCAGAAAGCGGCTAACCAAGGAAGAAGATGCACTTGGGAGAAGCTCTCAGCCATAAAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC