Sequence
atgc intronic sequence ATGC exonic sequencegttaaatacacactcttttacttgagatattttttggattcatttacatgaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 2
gttaaatacacactcttttacttgagatattttt-tggattcatttacatgaa----gattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
| |||| | | | ||| |||||| | | ||| ||| || || | | | |||||||| || || || || |||||||| || || |||||||| |||||||| ||||| |||||||||||| | |||||| | ||||| ||||||||
-------gtaggatcttgtttccaaattttttccatggattaagtgccatttgtctcaattgagctgttatgtgatgtcagGAAGCCAAGGAGAAATTTCAGCAGCTTCAGAAGGTGATATCTATTCTTGGGGATGAGGAGAAAAGGGCATTATATGATGAGACTGGAATTGCTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 2
-------gttaaatacacactcttttacttgagatattttttggattcatttacatgaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
| || ||| | || | || | ||| | || || | || | || | || | | | |||||||| ||||| ||||| ||||||||||| || || ||||| |||||||| |||| ||||||||| || | |||||| | |||||| | ||||||||
gtaggatctcaagcacaaagcattatttttttccactcgtttagtgcaatgtatctcaaa--tataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
gttaaatacacactcttttacttgagatattttttggattcattta-catgaagattct--actattgt----tttgttac-agGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
|| || | || | | || ||| |||| | | |||||| ||| ||| | ||| | | |||| | ||||||| ||||| ||||| ||||||||||| || || ||||| |||||||| |||| ||||||||| || | |||||| | |||||| | ||||||||
gtagtat-ctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G885923_T01 (Zea mays), 3'ss of exon 2
gttaaatacacactcttttacttgagatattttttggattcatttacatgaagattctactattgttttgttaca--------gGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
|| || | || | | || ||| |||| | | |||||| || | | | | | ||||| | |||||| ||||| ||||| ||||||||||| || || ||||| |||||| | |||| ||||||||| || | || ||| |||||| | ||||||||
gtagtat-ctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatattgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTCGAGATGCAGAGAAAAGAGCTTTATAGGATATGACTGGCATCACTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 2
---------------gttaaata------cacactcttttacttgagatattttttggattcatttacatgaa---gattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
| |||| || |||||| | |||| |||| | | || || | |||| | |||| ||||| ||||||||||| || || |||||||| ||||||||||||||||| ||||| || ||||||||||| | || |||||||||| ||||| | |||||||||
caaccttttatatctcctgaatatgccatcatggtcttttcactagaatatattttaggtgttgacacttgtaattgattagtttcttgtgttgttgcagGAAGCTAAGGAGAAATTCCAGCAACTGCAAAAAGTGATATCGATTCTCGGGGATGAAGAGAAGCGAGCTCTCTATGATCAGACTGGTTGTGTTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 2
-------gttaaatacacactcttttacttgagat-attttttggattcatttacatgaa-gattcta-ctattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
|| | | || || | || | | |||| ||| | | || | | | | || || | | | | |||||||||||||||| ||||| ||||| ||||||| || || | |||||||| |||||||| ||| |||| || |||||||| ||||| | |||||||||
gtgttttgtctagtgtttcctgttgtcctctaattgatttattgaaattatagatgttagcggttgtaattgatcatcttttacagGAAGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATTGCTATTCTTGGGGATGAAGAAAAACGGGCCGTTTATGATCAGACTGGTTTTGTTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 2
-------gttaaatacacactcttttacttgagat-attttttggattcatttacat--gaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
|| | | || || | || | | |||| || | | || | | | | | | | | | | |||||||||||||||| ||||| ||||| ||||||| || || | |||||||| |||||||| ||| |||| || |||||||| ||||| | |||||||||
gttttttgtctagtgtttcctgttgtcctctaattgatttattaaagttatagatgtttgcggttgtaattgatcatcttttacagGAAGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATCGCTATTCTTGGGGATGAAGAAAAACGGGCTGTTTATGATCAGACTGGTTGTGTTGATGATG
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
---------------gttaaatacacactcttttacttgagatattttttg---gattcatttacatgaagat-tctactattgttttgt----tacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
| | || | || | | || | |||| ||| | | ||| | | | | | | || |||| | ||||||| || || || || ||||| || ||||| |||||||||||||||||||||||||||||||||||| |||||||||| ||||| | |||||||||
gtgcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATGMapped 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|19875304|gb|AU236135.1|AU236135EST: ACCATAAGTTGGCATTGAAGCTTCACCCTGATAAAAATCAGGATGATAAG GAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGT
genomic: ACCATAAGTTGGCATTGAAGCTTCACCCTGATAAAAATCAGGATGATAAGgttaaataca ... tttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagatattttttggattcatttacatgaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
ttgtttt CT-rich tract
atattttttggatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaatacacactcttttacttgagatattttttggattcatttacatgaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA