Sequence
atgc intronic sequence ATGC exonic sequencegttctgcacgtgctattgactgaattctcttttaacattgtggtcttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA08G10180.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 11
gttctgcacgtgctattgactgaattctcttttaacattgtggtcttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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-gtcaggccatgttctcaaaactatgtt-tgttggcagta-aatatttatattaactg---cctggaaattaatttagttttctattttt---ctgatagGATATATTTAAAGAATTCTATTTGAGCAAGTATAGTGGAAGGCGTTTGATGTGGCAAAACTCATTGGGTCACTGTGTATTAAAAGCAGAGTTCCCAAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 11
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 11
---------------------------------------------------------gttctgcacgtgctattgac-tgaattctcttttaacattgtggtcttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggcctt-cagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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gttagtatatggccttggtggtggtagtaaatattttaacgtcagtctgagtattttagtctgaatatttgtttaacctctcccctctttctgaatactttgtttaatgttctcccctctttctgaatactttgtttaatcctctccctcttctgacagGATATATTTAAAGAGTTCTATTTAAGCAAGTACAGTGGAAGGCGTTTAATGTGGCAGAATTCTTTGGGACACTGTGTCTTGAAAGCAGACTTTCCCAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
gttctgcacgtgctattgactgaattctcttttaacattgtggtct---tggtagtttgtgatcccttgacatggtcctttctttcc-tctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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---------gttttactaa--aagttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------gttctgcacgtgctattgactgaattctcttttaacattgtg-gtcttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggc-cttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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gtttggcagcctaagtgatggtttctttcaagttttggcgctgggcatatacttttatataattatctgattttttgggttttgtttttgtgttttt-ttttttttttcccctgttgggtgccacagGACATTTTCAAGGAGTTCTACTTGAGCAAATACAGTGGGAGGCGATTAATGTGGCAAAACTCATTAGGACACTGTGTTTTGAAAGCAGAGTTTCCAAAAGMapped 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|21285971|gb|BQ473842.1|BQ473842EST: GATGTTAGACTTCCTCATGAATTGAATGTTTACCAG GATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATG
genomic: GATGTTAGACTTCCTCATGAATTGAATGTTTACCAGgttctgcacg ... gggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
ccttgac putative branch site (score: 4)
tcctttctttcctcta putative PPT
tttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctgcacgtgctattgactgaattctcttttaacattgtggtcttggtagtttgtgatcccttgacatggtcctttctttcctctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG