Sequence
atgc intronic sequence ATGC exonic sequenceGAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagcatcattctaattaaactataatctatatttaataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata...
Basic information
species | Glycine max |
transcript | GLYMA10G39540.1 |
intron # | 18 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G059381_T02 (Zea mays), 5'ss of exon 4
-------------GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagcatcattctaattaaactataatctatattt---aataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata
||||| ||||||||||| ||||| ||| ||||||||||||| || || |||| | ||||| || ||||| |||||||| ||||||||| | | || | | | | | | ||| | || || | || ||| ||| | || |||| || ||
TGAAAACCTGCAGAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttttggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctttcatttagat---
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 5
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagcatcattctaattaaactataatctatattt---aataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata
||||| ||||||||||| ||||| ||| ||||||||||||| || || |||| | ||||| || ||||| |||||||| ||||||||| | | || | | | | | | ||| | || || | || ||| ||| | || |||| || ||
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttttggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctttcatttagat---
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 18
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaag--atagcatcattctaattaaactataatctatatttaataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata--
|| ||| || |||||||||||||||||||| || ||||||||||| || |||| | || || || ||||| ||||||||||| |||| | | |||| | | ||| ||| | || | | | ||| ||| || || | | | | | || ||| | ||| |
GAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAGgttttccaaaaaatcact-tgattg--ttatcagctgtttcttcactaaaatcaaatctcttggctcacaaagaataagcctacttcttactgat-gatacaaa
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaa-gatagcatcattctaattaa--actataatctatatttaataagaaacatggct---tctgaacttaccacccgttattaaattgatttctgtttaatata---------------------------------------------------------------------------------------
|||||| || |||||||||||||||||||| ||||| ||||| || || ||||||||||| ||||| || || || |||||||||||| || |||||| | || | | | | ||| | | || | | || | || | || | || || || ||| | | |
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 21
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgta-----agatagcatcattctaattaaactataatctatatttaataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata-------------------------------------------------------------------------------
| || | |||||||||||||||||||||||||||| || || ||| ||||| || |||||||| |||||||| ||||||||||| |||| ||| || | | || |||||| | | || | | | || | || | |||| | | || | |
ACGGGAGATTTTTGATGAAGATGGATGGCTACATACTGGCGACATCGGGTGTTGGTTGCCAGGTGGTCGACTCAAAATCATTGATAGgtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcag
upper sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 20
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgta-----agatagcatcattct--aattaaa-----ctataatctatatttaataagaa-acatggcttctgaacttaccacccgttattaaattgatttctgtttaatata
| || | |||||||||| |||||| |||||||||| ||||||||| ||||| || |||||||||||||| || ||||| ||||| | |||||| ||| ||| | ||||| | || ||| | | |||| || | ||| | || | | || ||
ACGGGAAATTTTTGATGAAGAAGGATGGTTACATACTGGCGATATTGGGTGTTGGTTGCCAGGTGGTCGTCTCAAGATCATTGACAGgtactttcgaaaagcatcgatctttgcttagaaaagttgataatttgtaattaccgatagtacattttttgagtactaaatttacggtgtcccatcagtt-------------Mapped 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|10843907|gb|BF067252.1|BF067252EST: GGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG GAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAA
genomic: GGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagc ... ttttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagcatcattctaattaaactataatctatatttaataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata
- - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacccg