Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgacaaactagttgctggttggttagatatcttttttcatgttctactcaatgttcacatcatttctgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45270.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g29990.2 (Oryza sativa), 3'ss of exon 7
gtaagt--gacaaactagttgctg-------gttggttagatatcttttttcatgttctactca--------atgttcacatcatttctg--tgatattgtttaccatgt-ttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
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gtaagtttgccgacgtagatattttgcatccactgggtagatatgttgtgttatccacctatcatgactgttaggtcaacatgatgtttgcttgccttctctttttgtgaacttccagGTTCCAATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACAT
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g19140.2 (Oryza sativa), 3'ss of exon 5
gtaagtgacaaactagttgctggttggttagatatcttttttca--tgttctactcaat--gttcacatcatttctgtgatattgtttaccatgt---ttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT--------------
| | || | |||| | | || | || | || | | | | || |||| || | || | | | ||| | |||||| | ||| | | || ||||||||||| || |||||||||||| ||||||| ||||| | | || |||||| ||| | | ||
---atttgtaa--tgtccactgggtagatatgttgtgttatccacctatcgtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g19140.1 (Oryza sativa), 3'ss of exon 5
gtaagtgacaaactagttgctggttggttagatatcttttttca--tgttctactcaat--gttcacatcatttctgtgatattgtttaccatgt---ttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
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---atttgtaa--tgtccactgggtagatatgttgtgttatccacctatcgtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACAT
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G420055_T01 (Zea mays), 3'ss of exon 4
---gtaagtgacaaactagttgctggttggttagatatcttttttcatgttctactcaatgttcacatcatttctgtgatattgtttaccatgt---ttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
|| | | | ||||| | | |||| || | |||| || | | || | | || | ||| || | | ||| | | | | ||||||||||||| | | |||||||||||||| |||||||||||||| ||||||| ||||| | | || |||||| | || | |
attgttgtttaagatgtagttattatgttgttatccatttatttttat--tatgctta--ggctacgtgattctattgcttatatttttcttataagctttcagGTTCCAATGCGACAGCATAAAGATTGCAATTTTTCTTATGCTGGACTGAAGACTCAAGTTCGATTGGCAATTGAATCTAAGAACTT
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv15s0048g00390.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------gtaagtgacaaactagttgc--tggttggttagatatcttttttcatgttctactcaatgttcacatcattt---------ctgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
| | | || | | | || || | | | | | | |||| || | || |||| ||| | | || || || || | || ||||||||| | ||||| ||||| ||||| || || |||||||||||||| ||||||||||| || || ||| ||| | | ||
gtaagttgtttcccaaggtttcactcttctcattatagccacctttacctcaattgtatgtatgggtcccatctaaaaggtctaggtgataatatgattattttgcactttactgagttctttgttgttttgattcttagACCCCAATGAAACAACATAAGGATTGTAACTTCTCGTACGCTGGTTTGAAGACTCAAGTGAGGCTGGCAATCGAATCCAGAAATAT
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ14006 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgacaaactagttgctggttggttagatatcttttttcatgttctactcaatgttcacatcatttc-tgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
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----------------------------------------------gtaagcaacatgcctggatccctttatttgactatgtaaacttgttctgacagGTACCAATGAGGTCCCATAAAGATTGCAACTTTTCGTATGCGGGACTGAAGACTCAAGTGAAGCTCACAATTGAATCTTTAAACAT
upper sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ12995 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgacaaactagttgctggttggttagatatcttttttcatgttctactcaatgttcacatcatttc-tgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
| | ||| ||| || | ||| ||| ||| | | ||||| ||||||| | |||||||||||||||||||| ||||| || ||||||| ||||||| ||| | |||||| | | | ||
----------------------------------------------gtaagcaacatgcctggatccctttatttgactatgtatacttgttctgacagGTACCAATGAGGTCCCATAAAGATTGCAACTTTTCGTATGCGGGACTGAAGACTCAAGTGAAGCTCACAATTGAATCTTTAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttctactcaatgttcacatcatttctgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
atattgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgacaaactagttgctggttggttagatatcttttttcatgttctactcaatgttcacatcatttctgtgatattgtttaccatgtttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA