Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 2
gtgagttttaagtactccaa-cgtctagctttctcggttaaaccgttatg-cgcatttcagat----gttaatggagtttct-tttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
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-------gtaagcatcctaaacttctttctcttgctgatgtgacattttgtcgcaatttagCTTATTATTGGTGAACTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 2
gtgagt---tttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagat----gttaatggagtttctttt-cttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
|| || || || | || | | | | || | | || || || || || | || || | || || || | ||||| | || || ||||| || || || || ||||||||||||||||||||||| ||| |||||||||||
gtaagcatcttaaatttctttatcttacattcttactgatgtgacattttgttacaatttagCTTATTATTGGTGAACTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 2
gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
|| || | | ||| | | | | || | | | | ||| | | | || ||| || || || ||| || | || || ||||| ||||| || || ||||||||||||||||| ||||| ||| |||||||||| ||||| ||||| || || || || | |||
gtaagcatcttggacttaatcctttta-ttgatgtgctgttctgttgcacttaaagcttataataa--gaattctttcatgtagCGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGTGCTGAATTTGAAGGGGCTGTCATTGCACTGTTTCATCTGTTGATT
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 2
----------------gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtt-tcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
| | | | || | | | || | | | | || || | | | | | | | | | |||||| | || || ||||| || || || || ||||||||||||||||||||||| ||| |||||||||| || || ||||| | ||||| || | |||
tgtggcacatttagccacaaaccaaacaggccctaaatgccacatctcattgattagctattctgtatgtg-cggcttacggtaaactcatgtccatgtagTGAGAATATCATCTGGAAGGCGTTTAGCCCAACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGGGCAGTCATTGCATTGTTCCATCTATTGATT
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 3
--------gtgagttttaagtactcca---acgtctagctttctcggttaaaccgttatgcgcatttcagatgt-taatggagtttcttttct-tagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
|| | ||||| | | | || | || | | | ||| || | | || | |||| | |||| | |||||| | || || ||||| ||||| || || ||||||||||||||||| ||||| ||| |||| ||||| ||||| ||||| || ||||| || | |||
gtaagcatgttggatttaatccttttattgatgttgatattagattgatgtaatgttctgttccacttagtcttataataagactgctttcatgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGCGCTGAATTCGAAGGGGCTGTCATTGCACTGTTCCATCTGTTGATT
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtgagttttaagtactccaacgtctagctttctc-ggttaaaccgttatgcgcattt-cagatg--ttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
|| | | | | || || | || || || | ||| | || || | || | |||| | ||||| | ||| || ||||||| ||||||||| || |||||||||||||| |||||||| | ||||| ||||||||||||||||| ||||||||||| |
gcacaacctcctgtaactgtctgaagatgcattgttgattttcttctggagtatttcttacgtcggttaacaagttcctttctccggttttgtcctgcagTGAGAACATCATTTGGAAAGGATTCAGTCCGACCACCATCAACAGTGGTCGTGGAGCAGAGTTTGAGGGAGCTGTTATTGCTCTCTTCCACCTTCTGTTC
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttt-tcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
| |||| |||| | | || | ||| ||| || | | || | | ||| ||| || ||||||| ||| || ||||| ||||| || || || || ||||||||||| ||||||||| | || || || |||||||||||||| ||||||||||| |
cagcgcagcaattacattttatttaggtacacgtagtcctggtcctctgatttacttagtgaactgatcaagggaatctgctaatgttgatttctcgcagTGAAAACATCATCTGGAAGGCATTTAGCCCAACTACTATCAACAGTGGTCGTGGAGCTGAGTTCGAGGGCGCTGTTATTGCTCTCTTCCACCTTCTTTTC
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 2
gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgc---atttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
| | ||||| || | | || ||| || | | | ||||| | ||| || ||||| || || ||||| || |||||||||||||| ||||||||| | || || |||||| | |||||||| |||||||| | ||
-------------------------------gtgagagaaacctttttcttttcaagctctgattttttctattgtatctgtgacagTGAGAACATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTCGAGGGAGCTATCATTGCTCTGTTCCACCTCTTGATC
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 2
gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
| | |||| | || | | | || ||||| ||| | || ||||| | ||| || ||||| || || ||||| || |||||||||||||| ||||||||| | ||||| |||||| | |||||||| |||||||| | ||
----------------gtgagagaaaccttttcc--ttttccagctctgattatttctattgtgactgtgac----------agTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTTGAGGGAGCTATCATTGCTCTCTTCCACCTCTTGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
tgttaat putative branch site (score: 3)
tttcttttctt putative PPT
atgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttagTGAAAGCATTATATGGAAAGCATTCAGTCCTACAACCATCAACAGTGGGCGTGGAGCTCAATTTGAAGGAGCTGTTATTGCTCTTTTCCACCTTCTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT