Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
Basic information
species | Glycine max |
transcript | GLYMA15G11890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
----------gtgagttt-tgtgaggctacatgttta----ctata-cgattaatttgaacgcttgtatatcttctta--taagtcca--aagagtaattcagttta----cttacatg-----gtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
| | ||| |||| | | | |||| || || | | | ||| ||| || || || | || | | | | | |||| || |||| | |||| |||||||| ||||| || | || || || || ||||||||||| ||||| |||||||||||||| |||||||| || |||||||| |||||||||
gtatatctttgcgcttttatgtgcaaatgcttatttaatccctttatctgcctttcagggtatttggctattttgttgcctagtttcactagcattttcttattttaaattctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
------------------gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagt--ttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
| | ||| || | ||| ||| | | | | || | || || || | | | | | | | | | || ||||||||||||| ||||| || || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||| |||||||||| |||
gtatgtctctgggctctggccatgtttatgt--tcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
||| | | || || | | ||| | | | |||| | | | ||| | || || |||||||| | | | | || ||||||| ||||| ||||||||||| |||||||| || ||||||||| | || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |
----gttgaatatttttttgtggtt-tgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
||||| |||| | | || | | || ||||| || | || | | || | | | ||||| | | | ||||||| ||||| |||||||||||| |||||| || |||||||| || |||| |||||||| |||||||||||||| ||||| ||||| |||||||| |
---------gtgaga-tacacactcaatacatgtatat----ggttcttgtggatttgtttttca--tcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
|||| | | | || || ||| ||| | | ||| | | || | || | | | |||| |||||||||||||| || ||| |||||| |||||||| || | || ||||||||||| || ||||| ||||| ||||| ||||| ||||| |||
---------------------gtttcttgtg----tttttccaatagcagtaatggctctca---gctcaatcaat------gtgtttttgcctt-tgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGT
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttct-tataagtccaaagagtaattca-gtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
|| || || | | | || | | || ||| | || | || | | | |||| |||||||||||||| || ||| |||||| |||||||| || | || ||||||||||| || ||||| ||||| ||||| ||||| ||||| |||
------------------------------------gtttcttgcgtttttccaatagcagtaatggctctcagctcaatcaatgtatttttgccttttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGTMapped 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|16347925|gb|BI973520.1|BI973520EST: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG TTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTT
genomic: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAGgtgagttttg ... catggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTT
EST:
gi|17021880|gb|BM092914.1|BM092914EST: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG TTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTT
genomic: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAGgtgagttttg ... catggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
tacttac putative branch site (score: 1)
atatcttcttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG