Sequence
atgc intronic sequence ATGC exonic sequence...tccactaccaaccaaccaaaagacaagcatgcacgtgcatatgttgaaagtatatgattttatgaagcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT
Basic information
species | Glycine max |
transcript | GLYMA10G43720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38680.1 (Oryza sativa), 3'ss of exon 2
tccactaccaaccaaccaaaagacaagcatgcacgtgcatatgttgaaagtata---tgattttatgaagcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT---
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tatatt-ttaatctttgtatggctatgtatcttatgacagaagccggagatgtaatccatttgcattatctaaaaatatattttg-atctttgtg-gcggcagTATGGAAGGAGCTGGAGAAGGAGAACAAGGAGTTCTTCGAGACCTACAACAAGGACAGGGCGGAGCGCAACATCGAGGC---GGAGACGATGCAGCGGATCCA
upper sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------tccactaccaaccaac--caaaagacaagcatgcacgtgcatatgttgaaagtatatgattttatgaagcatggatataatacgtatggatacgtgctt-cagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT---
|||| || | ||| | | | ||| | | || ||||| | ||| | | || ||| || | | | || ||| | |||||||||||||||||||||| || |||||||| ||||||||| | |||| ||| || || | || || | | ||| || | |||
gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagat-tatat-tgttgttgttctattctatcatttcatgtggtctgaaaaagcacac-cacatgcatgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAG--GACCGCGAGGAGCGGAAGGTGGAGGC-GGAGACGATGGCGCGGATCGA
upper sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------tccactaccaaccaaccaaaagacaagcatgcacgtgcatatgttgaaagtatatgattttatgaagcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT-----
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gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtat--cgatctcattgacctcttcttggcattattatactatacatgc-tgc-tatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGT-----ATCTGGGACAAGAGTCGGCGCTGCAGAAGAATCCATCCGATGGACA
upper sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
tccactaccaaccaaccaaaagacaagcatgc-----acgtgcatatgttgaaagtatatgattttatga-agcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT
| | |||| |||| | || || | || | |||| | ||||| | |||| | | || || | | ||| || |||||||||||||||| ||||| || ||||||||||||||| || | || | || | || ||| | || |||||| |||||||||||||||||||
----aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatg--acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaagtatatgattttatgaagcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT
tatatgattttatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccactaccaaccaaccaaaagacaagcatgcacgtgcatatgttgaaagtatatgattttatgaagcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
-ccactac
- - - -ccaacca
- - - - - - - - - -aagacaag
- - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgga