Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22760.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
||| | | | | | | | | || | | | | || |||| | || | |||| || || | | ||||| ||| | | || |||||||||||||| ||||| || |||| || || |||||||| |||| |||||| ||||||||||||||||||||||||
gtaggcgctttt--tgctggatagtctgtactacttctagccctcatttc-catttatgtggtgctgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
||||| | | |||||||| ||| || | || | ||||| | | |||| |||| | || |||| || | | | |||||| |||||| | || || ||| |||| || || ||||||| |||| | ||| ||||||||||||||||||||| ||||
gtaagagcaca------ttccttttgcttttctt-----------ttctgtcatt--attgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
------------gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggt-tcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
||| | | | | ||| | || || | |||||| | || | | ||||| || || || ||||| ||| | | || ||||| ||||| || || ||||| |||| || || || ||||| |||| |||||| |||||||||||||||||||| |||
gtatggcgttgcgtacttctgttggagattgagatgtatgtacgtgtgttggc-catttactcccagaccgtggtgcttacattctacaatgaaatcgcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggc-tataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| || | ||||||| |||| || || || || |||| |||| | |||| | | || | ||||| || | | ||||||||||||||||| ||||||||| |||| ||||| ||||||||||||| ||| || |||||||| |||||||| ||||||
gtcagcaaatt-aatatttaactttattt-tctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| || | ||||||| |||| || ||| || | ||||| ||| |||| | | || | ||||| || | ||||||||||| ||||| ||||||||| |||| ||||| ||||||||||||| ||| || |||||||| |||||||||||||||
gtcagcaaatt-aatatttaactttatttttcactttcta---atttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| | | || ||| || | ||| | | | | | || | ||| ||| || | | || || |||| || ||| |||||||||||||||||| ||||||||| |||| || |||||||| ||||||| ||| || |||||||| |||||||| ||||||
----gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttatagg-tattaattattatctt--tttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
----gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
| || | || | | ||| || || | || || | | | || ||| || | | || || ||||| || ||| |||||| ||||||||||| |||||||| |||| || |||||||| ||||||| ||| || |||||||| |||||||| ||||||
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccacctttt--------atgggtattaattattatctt--tttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| || | | | | || |||| | |||| || | || | | | || | || | | || | ||||| || | || ||||||||||||||||| ||||||||| |||| || |||||||||||||||| || || |||||||| || ||||||||||||
gttag-gacataattcttgccttgtgtttata-----cagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
aatacatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA