Sequence
atgc intronic sequence ATGC exonic sequence...aaatatcttctatgctggtttgtccatgcttttgttgtagttgtgattcttctgcttttcttttattaacctcctaacctctccatggttgtttaaccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTTAAGACCTTATCAGTACTTTTCCTCATTGGTTTTGTTTCCATAGCTCCAA
Basic information
species | Glycine max |
transcript | GLYMA20G31540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31540.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G71940.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------aaatatcttctatgctggtttgtccatgcttttgttgtagttgtgattcttctgctttt--cttttat-taacctcctaa-----cctctcca-----tggtt--gtttaac-cagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTTAAGACCTTATCAGTACTTTTCCTCATTGGTTTTGTTTCCATAGCTCCAA
| ||||| | | | | | || | |||| ||| ||| ||| | | || ||| | | || || | ||||| ||||| ||||||||||||||| |||| ||||| || || | || ||||| |||||||| ||||| || ||||| ||||||||||| || ||| | || || |||||
gtaagctcttttacctccatccttcaccatctttccgcttatgatatgctatcattcaacattcctgtgtttcatctcttttcgccatctacataaagtgcgaagaacatggctttaaattctggttctgtttattgcagGCTGGCCTTGCTATTGGAGATCTCAAATCGGTGAAAGATCTGTATGATTTCAAGACATTGTCAGTGCTTTTCCTCATCGGGTTTATCTCTATTCTTCCAA
upper sequence: GLYMA20G31540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0072g01050.t01 (Vitis vinifera), 3'ss of exon 3
aaatatcttcta-tgctggtttgtccatgcttttgttgtagttgtgattcttctgcttttcttttattaacctcctaacctctccatggttgtttaa----ccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTTAAGACCTTATCAGTACTTTTCCTCATTGGTTTTGTTTCCATAGCTCCAA
| | ||| | | ||||| | | ||| | || ||||| |||| || | | || | || | | | |||| || | |||||||| ||||||||||||||||| |||||| | |||||||||||||||||||| || || ||||| ||||||||||| || ||| |||||||| ||| |
-----tttcctagtattattttgtgtaggacgttgaaaaaatttatgttctttgcttttttcttctgtgaactaatcactttactgttgttgcttgaatcatcagGCTGGGCTTGCTCTTGGGGATCTCAAGTCAGTGAAGGATCTATATGATTTTAAAACTTTGTCAGTGCTTTTCCTCATCGGATTTATTTCCATACTTCCTAMapped 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|48575487|gb|CO036428.1|CO036428EST: TTTCGGCGACATTGATTGGGCTCGTTCCAGCCTCTTATATTACTGTCAGA GCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTT
genomic: TTTCGGCGACATTGATTGGGCTCGTTCCAGCCTCTTATATTACTGTCAGAgtaagcatct ... gtttaaccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTT
EST:
gi|23730593|gb|BU763383.1|BU763383EST: TTTCGGCGACATTGATTGGGCTCGTTCCAGCCTCTTATATTACTGTCAGA GCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTT
genomic: TTTCGGCGACATTGATTGGGCTCGTTCCAGCCTCTTATATTACTGTCAGAgtaagcatct ... gtttaaccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcttctgcttttcttttattaacctcctaacctctccatggttgtttaaccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTTAAGACCTTATCAGTACTTTTCCTCATTGGTTTTGTTTCCATAGCTCCAA
tcctaac putative branch site (score: 1)
ttttcttttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatatcttctatgctggtttgtccatgcttttgttgtagttgtgattcttctgcttttcttttattaacctcctaacctctccatggttgtttaaccagGCTGGCCTTGCTCTTGGGGATCTAAAGTCAATTAAGGATCTATATGATTTTAAGACCTTATCAGTACTTTTCCTCATTGGTTTTGTTTCCATAGCTCCAA
- - - - -ctatgct
- - - - - - - - - - - -ccatgct
- - - - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcc