Sequence
atgc intronic sequence ATGC exonic sequence...attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
Basic information
species | Glycine max |
transcript | GLYMA09G07930.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
--attaattattagctagg-atggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
| || ||| ||| | | | |||| | | | | | || | || || | | | || | | ||| |||||||||||||||| |||||||||||||| |||||||||||||| || || ||||| || || ||||| ||||||||||| || ||| | || | ||| ||
cttgctgtgtctacctacccatgttaactctcgat--taagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatg-atagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 2
attaattatta-gctaggatggttagttacg-atagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
|| |||| | | | | | | ||| | | || | || | || || | | | || | |||||| |||||||||||||| || ||||| |||||||| |||||||||||||| || || |||||||| || ||||| ||||||||||| || || |||| | |||||||
ctttcttatcatatctgaaaaaaaaatcatatataaattgtttgtagctgtaacattacc-ttgctgattctgtttggtgaataaaattgttttat-tatagCCGTGAGATGTTCAACAAGTGGCAAGCACAAAGATGGTGGGCTGAAAATTATGACAAAGTTATGGAGCTTTACAATGTACAGAGATTTAACCATCAAGCT
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G066672_T01 (Zea mays), 3'ss of exon 3
attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtga---actaaattaaggtttatattttatgta-tagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
| ||| | ||| || || || || | | | | || ||| ||||| | ||| || | | | | | | |||||||||||| || ||||||||| |||| |||||||||||||| || ||||||||||| || |||||||||||||||||||| | | |||||| |
-ccagatatggatgtgcatgcttgcctat--ctatttatgtagca-gttcttcgaataaccatgtggtcatctgctattttgcatgtaacggtgtgtatgctagCCGTGAGATGTTCAACAAATGGGAAGCACAAAGATGGTGGGCTGAAAACTATGACAAAGTTATGGAACTTTACAATGTGCAGAAGTTTAATCAAACTGTC
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G429658_T01 (Zea mays), 3'ss of exon 2
--attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
| | || || | ||| || | | | || | | | |||| | | || || || || | || | ||||| ||||||||||||||| |||||||||||||| ||||| |||||||| || || ||||||| | |||||||||||||||||||| ||| |||| | |
ttactgat-atggatgtgcatgcttgctcatctatttatgtagcagttctttgaataaccatttggttgtctgcttttttgcacgtaatggtgtatgt-tagCCGTGAGATATTCAACAAATGGCAAGCACAAAGGTGGTGGGCTGAAAATTATGACAGAATTATGGAACTTTACAATGTGCAGAGGTTTAACCAAACTGTC
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G037941_T01 (Zea mays), 3'ss of exon 2
attaattattagctaggatggttagttacgatagttcatatgata-tgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgta-tagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
| | | | | | | | | | ||||| | ||| ||||| || | || || | | | | | | | || ||||||||| || || |||||||||||||| |||||||||||| | || || || || ||||| ||||| |||||||| || || | | ||| |||||| |
-gtttcaggtgacgaaagtacaaactaagtgttttctgtatgacaatgacaacttaccagtttc-tgttgtgttccttcatgcatggactaatgcataatagCCGTGAAATGTTCAACAAATGGCAAGCACAAAGATGGTGGACTGAAAATTACGAGAAGGTCATGGAGCTTTACAACGTTCAGAAGTCTAACAGTCAAGTT
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
----attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
||||| || | || | |||| | | || ||| | | || | | ||| | || | ||| |||| || |||||| || || || ||||| | ||||||||| ||||||||||||| ||||||||||| || ||||||||||||||||| |||| || | || ||||||
gtaacttaatcatgacctt---ttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttt-tgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
upper sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 3
---attaattattagctaggatggttagttacgatagttcatatgatatgatgactta-acaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
| | || | | | || | | || || | | | | | || | |||| ||| ||| | ||| || | | | || ||| || || || ||||||||||||||||||||||| |||||||||||||| ||||| | ||| |||||||| |||||||| |||||| |||| || |||||
tgtaagatgcctttgtttaatggcaaaggtgcaat-gtgctctagttctcactgctcatacaagtgaagggt---tttgattggttgttgtttcctttgattagTCGAGAAATGTTTAACAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAATTATGATAGGGTCATGGAACTCTACAATGTTCAAAGGTTTAACCGCCAAGCCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|17023158|gb|BM094192.1|BM094192EST: TTCGTGTCGCTTCCCCGTGGCGGGAACCATCTCAAACGGATACGATTCAG CCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTA
genomic: TTCGTGTCGCTTCCCCGTGGCGGGAACCATCTCAAACGGATACGATTCAGgtacgtgctc ... ttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
aactaaa putative branch site (score: 2)
aactaaattaaggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - gatggtt
- - - - - - - - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtggtg