Sequence
atgc intronic sequence ATGC exonic sequence...tttcagttatgtttgttctaaactctttttaaatgcagtccaacacctgtaaatatctaattgcttccattctaatcagatttactcatgtggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
Basic information
species | Glycine max |
transcript | GLYMA01G04930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 5
tttcagttatgtttgttctaaactctttttaaa--tgcagtccaacacctgtaaatatctaattgcttccattc-taatcagatttactcatgtggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
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--ataatt-tgctatttattcacttgtttgagaattaaactgcaccacattcacttggtatattgcagtgttccaccacttcatcagttcatttctttctcagGTCACTTGACATCAAAGAGTGACGTGTACAGCTTTGGAGTGGTGCTACTGGAGATGATGTCAGGCAGAAGGTCAATGGACAAGAATAGGCCAAACGGTGA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 5
tttcagttatgtttgttctaaactctttttaaatgcagtccaacacctgtaaatatc-taattgcttccattctaatcagatt-tactcatgt-ggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
| | | | ||| | | | || || | || | || | | || | || || | |||| || || | | ||| |||| ||| | |||||||| |||||||| || |||||||| ||||| |||||||||||| || | || | || || |||||||| |||| || ||||||||
tgcaaatgaagttcaaacacagat-ttgttgcctttggtatttta--tgcgattttcattatgactcttggtataattttcttgtattttttccacttttcagGCCATTTGACATCAAAGAGTGATGTCTATAGTTTTGGTGTGGTGCTACTTGAGATGATGTCAGGGCGCAGGTCAATGGACAAGAACCGCCCAAATGGTGA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 5
tttcagttatgtttgttctaaactctt-tttaaatgcagtccaacacctgtaaatatctaattgcttccatt----ctaatcagatttactcatgtggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
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-atgagctgtgaa-attctgagttgtcatccgcatgtggtttataa--tgtaggtcttctattgatcccatttgttctgataaaatttttatatatcatct-cagGACATTTGACATCAAGGAGTGATGTCTATAGTTTTGGTGTGGTTCTACTAGAAATGCTGACTGGCAGAAGATCCATGGACAAAAACCGGCCAAATGGGGAMapped 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|6665967|gb|AW277426.1|AW277426EST: GGGTGATGGGAACCTATGGTTACGCAGCACCAGAATATGTCATGACAG GTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTG
genomic: GGGTGATGGGAACCTATGGTTACGCAGCACCAGAATATGTCATGACAGgtaagtttag ... tggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTG
EST:
gi|120493846|gb|EH222013.1|EH222013EST: TCGGGTGATGGGAACCTATGGTTACGCAGCACCAGAATATGTCATGACAG GTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTG
genomic: TCGGGTGATGGGAACCTATGGTTACGCAGCACCAGAATATGTCATGACAGgtaagtttag ... tggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtaaatatctaattgcttccattctaatcagatttactcatgtggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
ttctaat putative branch site (score: 2)
aaatatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcagttatgtttgttctaaactctttttaaatgcagtccaacacctgtaaatatctaattgcttccattctaatcagatttactcatgtggtttgcagGTCATCTTACATCAAAAAGTGATGTGTACAGTTTTGGAGTGGTACTACTTGAGATGTTGACCGGCAGAAGATCCATGGACAAACACCGACCCAATGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - -tgtttgt
- - - - - - - - - - - - - - - - -tgcagtc
- - - - - - - - - - - - - - - - - - - - caacacc