Sequence
atgc intronic sequence ATGC exonic sequencegttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G27240.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 11
gttctgc-acgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
|| || | || || ||| | | | || | || ||||| | | | | ||| || || | |||| | | | ||||||| || ||||| |||||| | ||||| || |||||||| ||| ||||||||||||| ||| | ||||| ||||| || || |||||||| || ||||
gtcaggccatgttctcaaaacta---tgtttgttggcagtaa-----atatttatattaactgcctggaaattaatttagttttctatttttctga---tagGATATATTTAAAGAATTCTATTTGAGCAAGTATAGTGGAAGGCGTTTGATGTGGCAAAACTCATTGGGTCACTGTGTATTAAAAGCAGAGTTCCCAAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 11
-----------------------------------------------------gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatgg-tcctttcttt---cctctatcgggcatt-cagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
|| | | || | | |||| | | || | ||| || | |||| || | |||| ||| ||||| | | |||||||| || |||||||||||| ||||||| ||||||||||| ||| | |||||||| ||||| | || || ||||||||||| ||||| ||||||||||
gttagtatatggccttggtggtggtagtaaatattttaacgtcagtctgagtattttagtctgaatatttgtttaacctctcccctctttctgaatactttgtttaatgttctcccctctttctgaatactttgtttaatcctctccctcttctgacagGATATATTTAAAGAGTTCTATTTAAGCAAGTACAGTGGAAGGCGTTTAATGTGGCAGAATTCTTTGGGACACTGTGTCTTGAAAGCAGACTTTCCCAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgat-tcccttgacatggtcctttctttcc-tctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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---------gttttactaaa-agttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 11
----------------------gttctgcacgtgctagtgactgatttct-cttttaactgtggtcttggtattttgagtgattcccttg-acatggtcctttctttcctctatcgggcatt-cagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
| | || || | | | | | | |||||| | || | ||||| || | ||| | | ||| ||||| || | ||| ||||| |||||||| |||||||| | |||||||||||||| || || | ||||||||||| ||| |||| || ||||| ||||| ||||||||||| ||||
gtttggcagcctaagtgatggtttctttcaagttttggcgctgggcatatacttttatataattatctgattttttgggttttgtttttgtgtttttttttttttttcccctgttgggtgccacagGACATTTTCAAGGAGTTCTACTTGAGCAAATACAGTGGGAGGCGATTAATGTGGCAAAACTCATTAGGACACTGTGTTTTGAAAGCAGAGTTTCCAAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 11
gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
| | | || || || | || | | | ||| || | || ||| ||| || ||||| | || || | ||||| ||||||| || || ||||||||||| ||||| | ||||||||||| ||||| || ||||||||||| |
---------------------------------------gtgcctcgtgttctggctatcaaaattcgcgttttgatttaattgtcatttctcgca----gGACATATTCAAGCAATTTTACTTGAGCAAGCACAGTGGCAGGCGGCTGATGTGGCAGAATTCTTTGGGTCATTGTGTTTTGAAAGCCGAGTTTCCCAAGG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 11
gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
| | | || || || | || | | | ||| || | || ||| ||| || ||||| | || || | ||||| ||||||| || || ||||||||||| ||||| | ||||||||||| ||||| || ||||||||||| |
---------------------------------------gtgcctcgtgttctggctatcaaagttcgcgttttgatttaattgtcatttctcgca----gGACATATTCAAGCAATTTTACTTGAGCAAGCACAGTGGCAGGCGGCTGATGTGGCAGAATTCTTTGGGTCATTGTGTTTTGAAAGCCGAGTTTCCCAAGGMapped 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|19346215|gb|BM891095.1|BM891095EST: CATATCCGCCCATGGATGTTAGACTTCCTCATGAATTGAATGTTTACCAG GATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATG
genomic: CATATCCGCCCATGGATGTTAGACTTCCTCATGAATTGAATGTTTACCAGgttctgcacg ... gggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATG
EST:
gi|31561323|gb|CD487161.1|CD487161EST: CATATCCGCCCATGGATGTTAGACTTCCTCATGAATTGAATGTTTACCAG GATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATG
genomic: CATATCCGCCCATGGATGTTAGACTTCCTCATGAATTGAATGTTTACCAGgttctgcacg ... gggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgattcccttgacatggtcctttctttcctctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG