Sequence
atgc intronic sequence ATGC exonic sequence...acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
Basic information
species | Glycine max |
transcript | GLYMA07G37050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
-acctttgtatctttatgtttttttccatctcttgattgctt-ctaagttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
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aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgttatacctattg--ttcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
acctttgtatctttatgtttttttccatctcttgattgcttcta-----agttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
| || | | |||||| | | | ||| | ||| | | | | | || | | | || | ||| ||| | | | | | |||| || ||||| |||| |||||||| ||||| ||||| || || || ||||| ||||| || ||||| |||||||| || ||||| ||||||||||||||
--ccttat-catatatgttgcatactacagcttaaatgcatttgttgccattcctatttcattctagcatccctt--taaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
||| ||| || ||| | ||| | || | | |||| | || ||| || | | || |||| ||||||||||| |||||||| || || | ||| | || ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||
------gtacgttt---cttgttttggacgtagagttgttaagggagcatgc-agacttgattattcctt---gaatgtttacattttggc--gctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
--acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattacttttta-gtgaaaactttcctaaaaatcatctt-----------cagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
| | | | | | || | | | | |||| || || | | | ||| ||||| | || | ||||| | || || | |||| |||||||| || || |||||||| ||| | ||| |||| || |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctc-aaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
tcctaaa putative branch site (score: 2)
tcatcttc putative PPT
tataattactttttag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
acctttg
- - - - - - - - - - - - ccatctc
- - - - - - - - - - - - - - - - - - tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctaaaaa