Sequence
atgc intronic sequence ATGC exonic sequence...ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA09G18840.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
-----------------------------------------------------ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatc-cagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
|| || | | || | || | | | ||| |||||| | || | || || || | | ||| |||||||||||||||| ||||| ||||||||||| |||||||| || || || || || ||||||||||| || |||||||| || || || ||||||||||
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 16
-------------------ttccttataa-ttggtcag--gttttgttgtgt----tgttggcagcgatttagtatatt--------taaaaatccagcatttacagctaccaaactgctttatatgat----ttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
| || ||| |||| ||| | | | | | ||||| | ||| | | | | || || | || ||| | | | | | ||| | || ||||||| |||||||||||| | || || ||||||| ||| | || || || | ||||||||||||||||| |||||||| |||||||| ||||||||||| |
gttgatatttttggcatttccctttgtaaattggacagttatcctactatatgaactgttga-aatgataaaatgaaatcgctgtgataggaaatggggcttcacaagttcacatgttttgtatcttatatttttcagGAGGACTTCTATGCTATAGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGTATATCAATGCATGGCATAACAGATCGCTATCTTTCTGGTCAGAAGG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 16
ttccttataattggtcagg-ttttgttgtgttgttggca-gcgatttagta-tatttaaaaatccagcatt-tacagctaccaaactgctttatatg----atttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
||||| || || |||| | | | ||| ||| | | |||| | ||| | | | ||| || || || ||| ||| ||||||||||||||||| || || |||||||| ||||| |||||||| || || || || ||||||||||| || ||||| || || || ||||| |||||||
--------aattgtgcattcttctgttttttcatgtgcacattattgtgcagtattgcagttgccaacttccttcagtgactgaaatgttttcccccttgtattccagGAAGACTTCTATGCGGTCGTAGATTGGGCTTATAAAATTGACCCCTTGCGTTGCATCTCAATGCATGGGATTACAGAGCGTTACCTTTCTGGACAGAAAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G060949_T01 (Zea mays), 3'ss of exon 4
ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagcatttacagctaccaaactgctttatatgatt-----tcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
| | || | | | | || || | || | | | | |||| | | || | || || || |||||||| || |||||| ||||| |||||| | || || ||||||| ||| | || || || | || ||||||||||||||| ||||||| || ||||| |||||||||||||
-tgcataatttagactaaatactgatgagccaagagctgagttacca-acattttgggctgcgttgttga--gccttcac-ttgttttatatggttccttttcagGAGGACTTTTATGCTTTGGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGCATATCAATGCATGGACTAACAGATCGGTATCTTTCTGGTCAGAAAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
-ttccttataat-tggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagc-atttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
||||| | |||| | | | | || | | | ||| || | | | | | | || | ||||| ||||| |||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |||||||| ||| | |||||||||||||
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtca---ttttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
||| | | | | | | || || ||| || | || || |||||||| || ||||||||||||||||||||||| || || |||| ||||| | || || |||||||| || | ||||||||| |||||||| |||| ||||
-------------------------------------------gtagcgtctatgtgatttc---gttgacgtctaacaca-------atctg-tttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatatttaaaaatccagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
tttatatgatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaccaa