Sequence
atgc intronic sequence ATGC exonic sequence...aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
Basic information
species | Glycine max |
transcript | GLYMA03G28970.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgat---agCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
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gacatgcatttatgtg-atattaactttcgttgacccaacctat-tccttcccttgttttattcaaattacaactaat-tcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
-aatactcttttttatttatttcatctgattt-tgtattatcataggtcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
|||| | | | | | | | || | | | | || || | ||| || || || || |||| | | | | |||| |||| || ||||| || || |||||||| || || |||||||| || ||||| |||||||| || ||||| |||||| | || |||||||||||
agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttg--attttgtatgatttattatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
-aatactcttttttatttatttcatctgattttgtatta--tcataggtcatagcctt-cttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
| || ||| || || ||| || |||| |||| || | || | ||| |||| | | | || ||||| | | || ||||| | ||||| || || || | || ||||||||||| ||||| ||||| | ||||| ||||||||||| ||||||||||| ||||||||||||||||
gtaagctttttcttcttccttttg-ctccttttatattgagtctattgacacaatcttgcttagttttc--ttgaattggttcttactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
upper sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------aatactcttttttatttat---ttcatctgatttt----gtattatcataggtcatagccttc-ttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
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gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaa-gccttttttatatatc-cttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
upper sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttctta-ccatgcaataatatctattctttgcattgcaaacttgat--agCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
||| | | | | | | |||||| ||| || || | | | || | | | ||| | | | || | | | |||| ||| |||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| ||||||||| | |||||||| | ||
-tcacttgtgtgtgtatgtatcatctaattg-gtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactg-gtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
ttcttac putative branch site (score: 2)
aataatatctattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - -catctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgca