Sequence
atgc intronic sequence ATGC exonic sequence...tgttccctttggagaaaattccattaactggggttcttcagagattacatagagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61250.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 1
tgttccctttggagaaaatt---ccattaactggggttcttcagagattac---atagagaaaagcttta-atctttataactttcttg--tcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
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--------taaaagaatacttgaccatttattctgtttttttttttttaacttaatattcatgacctctacgtttccatagatttataagattaattttcacttt-cagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39720.1 (Glycine max), 3'ss of exon 1
tgttccctttggagaaaattccattaactggggttcttcaga-gattacatagagaaaagcttta-atctttataactttcttg--tcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
| | |||| | | | | | || | | | ||| | | || || | | ||| ||| | | | | ||||| | ||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||| | ||||| || ||| ||| ||||| ||||| ||
---acaaataaaagaatacttgaccgtttattctgttttatttaacttaatattcatgacctctacgtttccatagatttataagattaattttcacttt-cagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAATTATCTCAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G07960.1 (Glycine max), 3'ss of exon 1
tgttccctttggagaaaattccattaactggggttcttcagagattacatagagaaaagctttaatctttataactttctt---gtcggtcatggtgaaac---------agGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
| | || | || | | || | || || | ||| || ||| | ||| |||| ||| | | | || | |||| | ||||| ||||| ||||||||| |||| |||||||||||||| || |||||||| || || | ||| | || || ||| ||||| ||||| |
-----------caattcactcgtccatttgtagatttttaattttttcacat-gaacagttttgtttttttatacttgctttacataacttgcatttaaccctccctttcagGTCTTCTTCGTTGTGGCAAGAGTTGCCGGCTAAGATGGACAAACTACCTCAGACCAGATATTAAACGTGGTTCCTTTACACTTGAGGAAGAAAAACTAAT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 1
tgttccctttggagaaaattc----cattaactggggttcttcagagattacat-agagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
|| | || ||| ||| ||| ||| | || || | | | | || | || | |||||||| | | | | | ||||| | ||||| ||||| ||||||||| || | |||||||||||||| || |||||||| || || | ||| | || || ||| || || ||||| |
----ccatctgtagatttttcttcacatgaacacttttgtttttatacttgctttacataagaatatttggccatataacttcccttttaaccctcccttt-cagGTCTTCTTCGTTGTGGTAAGAGTTGCCGGTTAAGATGGACAAACTACCTCAGACCAGATATTAAACGTGGTTCCTTTACACTTGAGGATGAAAAACTAAT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g03190.t01 (Vitis vinifera), 3'ss of exon 1
---tgttccctttggagaaaattccattaactggggttcttcagagattacatagagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
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tatcaactctgtttatcctcattttacttccttgaacccataatgttttcgattttgatatattatggggttcggg---ttcttggctttcctctttcaacagGTCTCCTCCGCTGTGGGAAAAGTTGCAGACTCCGATGGACCAATTATCTTAGACCAGACATTAAGCGAGGACCCTTCACTACTGATGAAGAGAAGCTTGT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 1
tgttccctttggagaaaattccattaactggggttcttcagagattacatagagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
| || | || | | ||| | ||| ||||| | | || || | |||| | |||||| || ||||||||||||||| ||||||| |||||||| | || || ||||| |||| |||| || | |||||| ||
----------------------------------------gtgaatcgatttctcacatcttcg--tctcatag-tttctcttggatcttg--cgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAACTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatagagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
ttataac putative branch site (score: 2)
tttaatctttataact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttccctttggagaaaattccattaactggggttcttcagagattacatagagaaaagctttaatctttataactttcttgtcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - -gagaaaa
- - - - - - - - - - - - - - - - - - - - - - - acataga
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaagc