Sequence
atgc intronic sequence ATGC exonic sequencegtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34410.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctga-gttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtc-----tttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
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-------------------------------------------------------------aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttt---tgccaacttttaggtaag---atttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|| || ||| | || | ||| ||| | | || ||| | |||| ||| || | | ||| ||||| | || | |||| ||| |||| ||||| | ||||| ||||| || || || ||||| | || ||||| |||||||| |||| |||||||||||||| |||||||||||||| || ||||| |
----------------------------------tagcacttttatat-tctttctcgctgtt-----gtat-tatgcaatccttttagtact-tgtatgttggctttaagtgtgctataattattttatctgc-------------------ctttccagGTCTTGTTTCTGATGTACCACTATTTCGCTGCCACAGAAATATACAATGCAATTCGGGTGTTCATTGCTGCCTATGTCTGGATGACTGGATTCGGGAATT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 1
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
| |||||| | | || ||| ||| ||||| ||||||| ||||| ||||| |||||||| |||||||||| ||||||||| | || ||||||||| ||| |||||||||||||| |||||||| |
------------------------------------------------------------------------------------------------------------------------------gagtgtactaatt---attcgttctgtgtttccagGTCTTATTTCTGATGTACCATTATTTTGCTGCTTCTGAGATATACAATGCAATCCGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttcca-tgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|| ||||| ||| ||| || | ||| | || ||| ||| | | | | | |||||| | |||| | | | | | ||| || | ||| | | || | || || ||||| | ||||| ||||| || || || ||||| | || ||||| ||||||||| | || ||||||||| ||| |||||||||||||| |||||||| |
-----------------------gttggtgatatta-catcaat-cacttctttagttctccttggcaatgtggttttttagctatctatatcacc----ggagtttggagaggctcttgattgtgttgaaatgcccaatgcattttaatatgcaattccagGTCTTGTTTCTGATGTACCACTATTTCGCTGCCTCGGAAATATACAATGCAATCCGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 7
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|| | | | | || || ||||| || | | ||| |||| | | | || | || | | | || || || | | | ||||| || ||| | ||||||||||| |||||||| | |||||||| |||||||| | |||||||||||||| || || ||||||||||| ||||| ||||
--------------------------------------------------attcattagaaacttagaaactacat-----tttttcagttttaattttgtctgttatttctaagtaatggtt--catctgttcaagctt----ttgttccatttgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 7
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|| | | | | || || | ||| || | | ||| |||| | | | || | || | | | || || || ||| | ||||| || ||| | ||||||||||| |||||||| | |||||||| |||||||| | |||||||||||||| || || ||||||||||| ||||| ||||
--------------------------------------------------attcattagaaacttagaaactacat-----tctttcagttttaattttgtctgttatttctaagtaatggtt--catctgttcaagctt----ttgttccatctgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 1
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgct--aatttacagtttttgtgtctttg-cagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|||| || || ||| || || | || ||| || | | | || ||||| ||| |||| | ||| | | ||| |||||||||||||| ||||| || ||||||||||| || |||||||| |||||||| | || || |||||||| || |||||||||||||| ||||| ||||
-------------------------------------------------gttttactttatttttattatctattattg---cttgcaatgccattgttacatagtgcaatttgcctcaaataattttctgagcttggatttgtcttctttttctttttaacagGTTCTATTTCTAATGTACCACTACTTTGCTGCTGCGGAGATATACAATGCAATTCGTGTCTTTATTGCTGCATATGTCTGGATGACTGGATTTGGAAACT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S357_34V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgc-taatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
|||| | | | | || ||| | | || | | || ||| || | | || |||| | | | | ||| | ||||| || |||||| || || || |||||||| || || | || ||| | |||||||| || | ||||| |||||||||||||| |||||||| |||||||| ||||
-------------------------------------------------ttttcaccgccaccttcgaggataa---taaacttgtacaaagcatatttg------ttacattcacttcatttgttcttctgacatcgtttggatttttttcgt----gcagGTCCTTTTCCTCATGTATCACTATTTCGAAGCTAAAGAGTTTTATAATGCCATTCGAGTTTTTATTGCTGCCTACGTTTGGATGACGGGGTTTGGCAACT
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S74_21V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
||| || | | | | | ||||| | | || || | ||| | ||| || | | | | | | |||||| || | | || ||||| || || ||||||||||| ||||| | || ||| | || ||||| || |||| ||||||||||||||||| |||||||| || ||||| ||||
-----------------------------------------------------tgcgacttgtgaattgttaagaagaaagtttatcgttagttcgat--gatttaacctgttcactgaatttataatgta---ttatttac---ttgtctaaaatttcagGTCCTTTTCCTTATGTATCACTACTTCGAAGCAAAGGAGTTTTACAATGCTATTCGGGTGTTCATTGCTGCCTACGTTTGGATGACGGGTTTTGGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
tgctaat putative branch site (score: 2)
tgtcttt putative PPT
taatttacagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC