Sequence
atgc intronic sequence ATGC exonic sequencegttagtctcatttcatctaatatgccatagtgtttgcgaaatcgattacttactgcttttcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53130.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 6
-------------------gttagtctcattt--catctaatatgccatagtgtttgcgaaatcgattacttactgctttt-----cttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
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ttttttttgtttttttttcctcatttttgcttagaaactagtttcaaacctgggtcaagtattcttctactttttgactctaatatcttttttggaacagACATATTTGCAGTCAACAACCACCAGATTGGAGGAAATGAGGGTGAAAAGGAGAGATGCAGAACAGTGGATGTCCCATCGATTACTTCCTGACAGCCTGA
upper sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 6
---------------gttagtctcatttcatctaatatgccatagtgtttgcgaaatcgattact-tactgcttt----------tcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
|| | |||||| || | || | | | | | || | | || |||| |||||| ||||| ||| |||| || || ||||| ||||||||||| |||||||| || || ||||| |||||||| |||||||| || || || || ||||| | | | |
ctcaatctttttttttttctccacatttctgcttggaagctagtttcaaacctgggccaaatattcttctactttgactctaatatcttttttggaacagACATATTTGCAGTCAACAACCACCAGATTGGAGGAAATGAGGGTGAAAAGGAGAGATGCAGAACAGTGGATGTCCCATCGATTACTCCCTGACAGCCTTA
upper sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G31940.1 (Glycine max), 3'ss of exon 5
----------------------------gttagtctcatttcatctaatatgccatagtgtttgcgaaatcgattacttactgcttttcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
| || | | ||| |||| | | || || || || | | || ||| || ||||| ||| |||| || || ||||| ||||||||||||||||| ||||| || || || |||||||| |||||||| || || ||||| || || | ||
ttgccaagcaaaacacaatttattaattagaaacctgagtcattctgttatgaggttatattcttcaaggttatcaccaattatacttggtttgaa--acagACATATTTGCAGTCAACAACCACTAGATTGGAGGAGATGAGAGTAAAAAGGAGGGATGCAGAACAGTGGATGTCTCATCGATTGCTTCCAGATGGCCTGC
upper sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gttagtctcatttcatcta--atatgccatagtgtttgcgaaatc---gattact-tactgcttttcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
| | |||| | | | | |||| || || | | || ||| | ||||| ||| | | | ||||| |||||||| ||||| |||| ||||||||||||||||| || || || |||| |||||||| |||||||| || || |||| ||||||| |||
aagagtgatgtgaggctcatgagatggtctggatgcctggaccatattttatggtactcatttagtcttgaattgatgtactgaatttgtggt--gtaacagACATATCTGCAGTCCACAACCATAAGATTGGAGGAGATGAGAGTGAAAAGGCGAGATGCAGAACAGTGGATGTCTCATCGCCTGCTTCCTGAGAGTCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgccatagtgtttgcgaaatcgattacttactgcttttcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
tacttac putative branch site (score: 1)
cttactgcttttcttt CT-rich tract
ttttcttttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctcatttcatctaatatgccatagtgtttgcgaaatcgattacttactgcttttcttttaaatggcagACGTATCTGCAATCCACTACCACGAGATTGGAGGAGATGAGGGTAAAGAGAAGAGACGCAGAACAATGGATGTCACACCGTTTGCTACCTGAGAACTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA