Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
Basic information
species | Glycine max |
transcript | GLYMA09G01050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
----------gtgagttt-tgtgaggctacatgtttactatacgattaattaattt---gagcacttgtgtatcttctt-tcaagtctaaaga-------ctaattcagtgtacttgcatg-----gtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
| | ||| |||| | | | |||| || | ||| | || | | | ||| ||| || || | ||| | | | || ||| | || |||| | |||| |||||||| ||||| || | || || || || ||||||||||| ||||| |||||||||||||| |||||||| || || |||||||||||||||
gtatatctttgcgcttttatgtgcaaatgcttattta--atccctttatctgcctttcagggtatttggctattttgttgcctagtttcactagcattttcttattttaaattctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
--------gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaa--gtctaaagactaattcagtgtacttgcatgg----tatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
|| | | || | ||||| | || || || || ||| | | || | || | | | | | | | ||| || | | | ||||||||||||| ||||| || || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||| ||||| |||| |||
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaattaatt-tgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
|| || | ||| | || | || || | | ||| | | ||| | || | || ||||| | | | | || ||||||| ||||| ||||||||||| |||||||| || ||||||||| | || ||||| ||||| ||||| || ||||||||||| |||||||||||||| |
---------gttgaa-tatttttttgtggtttgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
||||| |||| | | || | | || ||| | | |||| | || || || | | || || | || |||| | ||||||| ||||| |||||||||||| |||||| || |||||||| || |||| |||||||| |||||||||||||| ||||| |||||||||||||| |
---------gtgaga-tacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctgagt----tttaatggactt------ttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggt-atagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
|| | || | | | | | | || || | ||| ||| || | |||| |||||||||||||| || ||| |||||| |||||||| || | || ||||||||||| || ||||| ||||| ||||| ||||||||||| |||
----------------------------------------gtttcttgtgtttttccaatagcagtaatggctctcagctcaatcaatgtgtttttgcctttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtactt--gcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
|| || || | | | | | | || || | ||| |||| || || | | |||| |||||||||||||| || ||| |||||| |||||||| || | || ||||||||||| || ||||| ||||| ||||| ||||||||||| |||
----------------------------------------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|5342441|gb|AI794725.1|AI794725EST: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG TTTAAGCAAGCGGAA
genomic: GCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAGgtgagttttg ... catggtatagTTTAAGCAAGCGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
gactaat putative branch site (score: 2)
actaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG