Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01960.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
--------------------gtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctct----tatttat-accctgtttg--ttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
| ||| | | || | ||| | | || | | | | | | | | ||| | ||||| || | | |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| | |||||||| ||||| || |||||||| || || || ||||| |||
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 7
-----------------------------gtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
|| |||| | || ||| || |||||| || || || | | |||| | | |||| | || ||||| || || ||||||||||| |||||||| ||||| || || |||||||| | |||||||| ||||| || |||||||| || || || || || ||
gtaaggaatctgaggctttattatcattactacattgcaatgtgtttttttacatttctgttcggtctt-atagacagtgcatgattttttttttttttgccctcttg-tagGCATTACAATATGAACCGCATCAGACTTGTTTGGTCAAGTATATGGCATGTCTTGTCTGATTTTTTTGTCACCATTGGCTGCTCAGAAAATCTTTCAATC
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
------------gtaagg-atcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgta----atggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
| | | ||||| | | | ||| | | || || || || | | || || | | || | || | |||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||||| | ||||| || |||
acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
------------gtaagg-atcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtt--tgttgtaatg--gcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
| | | ||||| | | | ||| | | | || || || | | || || ||| ||| || | ||| |||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| ||||||||||||| | ||||| || |||
acaaatgtttgggcagagcatcaagcatatgattatgttgcatcattgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 7
------------gtaagg-atcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttat-----accctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
| | | ||||| | | | ||| | | || || ||| || | | || ||| | | || | || || | | |||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||||||||| | ||||| || |||
ccaaatgtttgggcagagcatcaagcatatgattatgttgcatgattggttgatgtttatatgctgctatctgttgtttgacccgattattatg-taacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTTTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
----gtaaggatcaatcttttctttacgatatctgttttgtttttgctcact-ctctcttatttataccct----gtttgttgtaat--------ggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
| ||| | | |||| | | || | ||| |||| || |||| ||||| | |||| | || |||||||||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||||| ||||| || |||
gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattattctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G45360.1 (Glycine max), 3'ss of exon 9
gtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT-----------------------------------------------------------
| | | || | | | || | || || || | | |||||||||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||||||||||| || ||||||||||||| ||||| || |||
----------------------------------------taattatactgtttgactt-tgaggtgattattctg-taacaggcactataatatgaaccgcatcaggcttgtgtggtcaagcatatggcatgttctctcagATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATTGCAATTTTTGCAATGGATTCCTTGCGTCAGTTGTCAATGAAATTTCTGGAGCGGGAGGA
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------gtaaggatcaatcttttctttacgatatctgtt--ttgtttttgctcactctctcttatttataccctgtttgttgtaatg---gcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
|| | || ||| || |||| ||| || | || | | | | || || |||||| | | ||||||||||||||||||||| || || ||||| ||||| |||||||||||||| ||||| ||||||||||| || ||||||||||| || ||||| || |||
gtatgaatcattctcaatttgtcttgttcatgttttagcataccatattagtgcttcatttattatttatatttgtcagctgctattaaaaattttgctaaaattctaagtgatttgttttcttttacacagGCACTATAACATGAACCGTATCAGGCTTGTGTGGTCAAGCATCTGGCATGTACTCTCAGATTTCTTTGTAACCATTGGCTGTTCAGAGAACCTTTCAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttttgtttttgctcactctctcttatttataccctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
tgctcac putative branch site (score: 2)
tcttatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT