Sequence
atgc intronic sequence ATGC exonic sequence...tttcccagccagtcgctgcttccaaatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
Basic information
species | Glycine max |
transcript | GLYMA10G41110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 4
-----tttcccagc-cagtcgctgcttcca-aatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
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tgattagagatagcgcattcattggtcctttgatgtgacaaaagtgca-aaacataagtgagat---tgcataaactttgttcaca---tatgtgccatccttttagGTCTTGATGCGTTCCAGGCAGAGAAGGTCATGGAAACTCTTAGACAGCTTGCAGAAGATGGACACACGGTGATATGTTCTATACATCAGCCAAGAGGTTC
upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 4
tttcccagccagtcgctgcttccaaatg--cggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtg-ctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
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--tcataaacagtagtcatcaacatctgtttggtcatctgaca-atatgaaaatgtcaaatattaagttatatttttttgtatgtatgtgatttgtcttttagGCCTTGATGCCTTCCAAGCTGAGAAGGTCATGGAGACTCTTCGTCAACTTGCTCAGGATGGGCACACTGTTATCTGTTCGATACACCAGCCAAGAGGTTC
upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
----tttcccagccagtcgctgcttccaaatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
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gtaaatgcctagtctgt--ctgattctgaacattgatggattgttttaaaaa--agaa-----------ttagaggatgataaaatattcttgtg-gtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 4
---tttcccagccagtcgctgcttccaaatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
||| | | || | || | | | | | | || || | || || | | ||||| | || | | |||||| |||||| ||||| |||||||| || || || ||||| || |||| || ||||||||| ||||| || |||||||||||||| ||||| ||||| ||| | ||
ttctttttttctccataactattggcatgagagttttgctagtagtgaagcccacataagct-tcta--tggtttgtaaccaaataactgatggtgcttgtagGACTCGATGCTTTCCAGGCAGAAAAGGTGATGGAGACACTCCGACTACTTGCACAGGATGGACACACTGTAATTTGTTCCATACACCAGCCTAGAAGTTC
upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ08843 (Selaginella moellendorffii), 3'ss of exon 4
tttcccagccagtcgctgcttccaaatgcggtcaatttgcac-agacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
| | |||| | | || | | || || | | | || | || || || || ||||||||||||| || || || ||| |||| |||||||||||| | ||||||| |||||||||||||| || | ||||| || |||||||| | || ||
-----------------------------gtttgttttgtgctacgcagtttcggagt-----catttctgattccttggactttttcccttggc---cagGACTTGATGCATTTCAAGCAGAGCAAGTGATGGAAACTCTCAAGAAACTTGCCCAAGATGGTCATACCGTTGTGTGTTCGATTCATCAGCCTCGTGGATCMapped 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|193386904|gb|FK351761.1|FK351761EST: TTATATTTGCTGATGAACCCACAACAG GACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTG
genomic: TTATATTTGCTGATGAACCCACAACAGgtaatcatgc ... gtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
tcataac putative branch site (score: 2)
ttttctgtgctttc putative PPT
acttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcccagccagtcgctgcttccaaatgcggtcaatttgcacagacaatcataacctctctccacttattttgtcatgaagttgttttctgtgctttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCTATACATCAGCCAAGAGGGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- -cccagcc
- - - - - - tcgctgc
- - - - - - - - - - - caaatgc
- - - - - - - - - - - - - - - - - - - -cacagac