Sequence
atgc intronic sequence ATGC exonic sequencegtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10170.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 7
gtgattaattttactattaattataat-------tatccaatctaacaaa----tcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| ||||| | || ||| | | ||| | || || ||| | || |||| | || || | ||||||||||||| | ||| |||||||||||||| |||||||| || ||||| |||||||| |||||||| || |||| ||| || || |||||||||| ||||
gtttgcaatttgtccatggattcttctgcagcagtatgccattaaaaaaaaacttagttttggattaaaacttgtccatgtattcttctgcagTATGTGCCGTATGTTGGAGACAGCAAGAGGGCAATGGACGAGTACACCTCAGAGATCTTCATGGGGGGTAAGAGCACCATCGTTCTGCACAACACCTGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 7
------------gtgattaattttactatta-attataattatccaatctaacaaatcacattaacataaattatact-----attggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| | | |||| | | || || | | || | | || || | |||| ||||||||||| | |||| || || ||||||||||| || ||||| || ||||| || ||||| |||||||||||||||||||| || ||| |||||||||| || |
ctccgatagaatctgccagaccgaaaaattataccccgctgatgcacggtggctgatgatttggttgctgtttctattgagtaattgttaattgttgcagTATATTCCATACGTTGGGGACAGCAAGAGGGCCATGGACGAGTACACCTCGGAGATCTTCATGGGAGGGAAGAACACCATCGTGCTGCACAACACCTGCG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 7
-----gtgattaattttactattaattataattatccaatctaacaaatcacattaacat-aaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| | || || | | ||| || | || ||| || ||| |||| || | | | | |||||||||||||||| | || |||||||||||||| || ||||| || ||||| |||||||| |||||||| || |||||||| || ||| |||||||||| ||||
gtctgttagctgatctttcacctcgttaaaagttgacatat--gcaaggcagatttacattgaaacttgtcactcttt--tgttgcagTATGTGCCGTACGTGGGAGACAGCAAGAGGGCTATGGACGAGTACACCTCAGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 5
-----gtgattaattttactattaattataa--ttatccaatctaacaaatcaca------ttaacat-aaattatactattggat-ggtgt-tgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| |||| || | | ||| || | | || | || | | | || |||| ||| | | | | | | || ||||||||||||| | || |||||||| ||||| || ||||| || |||||||||||||| |||||||| || |||||||| || ||| |||||||||| ||||
gtctattagctaatcttccacctctttaaaaagctggcacatgcagcagtttaaacgtagatttacattaaaacttgccactcctttgctgcatgcagTATGTGCCGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGTGGCAAGAACACCATCGTGCTGCACAACACCTGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 7
-----gtgattaattttactattaattataa--ttatccaatctaacaaatcaca------ttaacat-aaattatactattggat-ggtgt-tgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| | || || | | ||| || | | | | || | | | || |||| || | | | | | | || ||||||||||||| | ||| |||||||| ||||| || ||||| || |||||||||||||| |||||||| || |||| ||| || ||| |||||||||| || |
gtctgttagctgatcttccacctctttaaaaagctggcacgtgcagcagtttaaacgtagatttacattgaaacctgccactcctttgctgcatgcagTATGTGCCGTATGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCGGCAAGAGCACCATCGTGCTGCACAACACCTGCG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 7
----------------gtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatggtg---------ttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| || | ||| | | | | || | | || | | ||| || ||| | |||| | || | |||||||| | || | ||| || |||||||||||||| ||||| ||||| || || ||||| |||||||| || |||||||| || ||| |||||||||| ||||
gtcggtcggtccacttgttgtttagtttgtgactgagtcta--tcccatatatgctacttcatgtttgattaattgttactcaaagttgatccctcttcttttgcagTACATCCCCTATGTGGGTGACAGCAAGAGAGCCATGGACGAATATACCTCCGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G010768_T01 (Zea mays), 3'ss of exon 1
------------gtgattaattttactattaattataattatccaatctaacaaat-cacattaacat--aaattatactattggatggtgt-tgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| | | | || || | | || | ||| | ||| |||| ||| | | | || || |||||||||||| | || |||||||| ||||| || ||||| || |||||||||||||| |||||||| | |||||||| || ||| | |||||||| | ||
atttgttagctgatcttccacctctttaaaaagcttgcaggtgcagtagtttaaacgtagatttacattgaaacttgccactcatttgttgcatgcagTATGTGCTGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCAGCAAGAACACCATCGTGCTACACAACACCTATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
--gtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| || || | ||| | | ||| ||| | | || | | | | ||| | |||||||||||||| | ||||| || ||||||||||| |||||||| ||||| ||||||||||||||||| || |||||||| ||||| |||||||||| ||||
gtatatttgtttcacccatttttcactatttctttctcttgtcaggt-ctttgattctatctgctttgttgcct----ttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 4
-----gtgattaattttactattaattataattatccaatctaacaaatcacatta---acataaattatact---attggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
| || ||||| |||| | | | || | ||| ||||| ||| | | | | ||| || || | |||||||| ||||| | |||||| ||||||||||| || |||||||| ||||| || |||||||||||||| || |||||||| |||||| |||||||||| ||||
gtaattttttttatttttttatttttagtcactactccctctttcaaattcaattggttatttttttgacactttggtttattgtttttgcagTACGTGCCTTATGTAGGGGACAGCAAGAGGGCCATGGATGAGTACACTTCTGAGATATTCATGGGTGGAAAGAACACAATTGTGTTGCACAACACATGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 6
gtgattaattttactattaatta--taattatccaatctaacaaatc----acattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| ||| | || || | | | | | || ||| || | | | | | || ||| |||| ||||||||||| || | || || ||||||||||| || |||||||| ||| | || |||||||||||||| || |||||||| |||||| |||||||||||||||
gtaatttttatttttagtcactcactctctttcaaattcaattggttctttatttgactcttcggtaattaatttattggttttgcagTATGTACCTTACGTTGGGGACAGCAAGAGGGCCATGGATGAGTACTCTTCTGAGATATTCATGGGCGGAAAGAACACAATTGTGTTGCACAACACTTGTG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 7
-----------------------gtgattaa----ttttactattaattataattatccaatctaacaaatcacattaacataaattatacta--ttggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| ||||| | || | | | || || | | | | | | ||| || || | || |||||||||||||| | ||||| || ||||||||||| |||||||| ||||| |||||||||||||||||
gtgaacatcccgaccatgttgttgttattaaggtatatttgtttcacccatttttcactatttctttctcttgtcagGTCTTTGATTCTATCTGCTTTGTTGCCTTTGCAGTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGT----------------------------------
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtgattaattttactattaatta--taattatccaatctaacaaat-cacattaacataaattatactat-tggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
|| || | || || | | | | | | || | || | || | | | ||||||| | | | || | |||||||||||||||| ||| ||||| ||||||||||| |||||||| ||||| || |||||||||||||| ||||||| ||| |||||| |||||||||| || |
gtatatcgcagaaccctccttttgtttgtatgtattacaattcagatgctggtttggactcattcattctcactggctaacattatacggtgttgttgatattgcagTATGTGCCATATGTTGGAGATAGCAAGAGAGCCATGGATGAGTACACTTCTGAGATATTCATGGGTGGGAAGAGCACCATTGTGCTGCACAACACCTGCG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 7
gtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatg--gtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
||| | | || | | || ||| | || | | || || ||||||| || | || || || |||||| | || ||||| |||||||| || ||||||||||||||||| | || ||| || | |||||||||||||| |
----------------------gtaa--aacaaacgcttgatttttttctagggaaaactcccgagtttgctttcgttttctagTATGTTCCTTACGTCGGTGATAGCAAGCGGGCCATGGACGAATACACGTCCGAGATATTCATGGGAGGCAGGAGCACCATCGCCATGCACAACACTTGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatccaatctaacaaatcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
cattaac putative branch site (score: 2)
aaatcacattaacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC