Sequence
atgc intronic sequence ATGC exonic sequencegtattgctgcacatatatatggcagtattgatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
Basic information
species | Glycine max |
transcript | GLYMA12G02200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 5
gtattgctgcacatatatatggcagtatt--gatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
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gtatagtctgtcgtct-tgtcacaaaatttgaacattgtgtgcatcgg-atccatgtcagttgacataatgttctctcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG
upper sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090338_T01 (Zea mays), 3'ss of exon 5
gtatt-gctgcacatatatatggcagtattgatttg---atggagat-cactaatcagga-------tacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
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gtatttgtctgacatat-tgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG
upper sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02330.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtattgctgcacat-atatatggcag-tattgatttgatggagatcactaatcaggatac-ttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
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gtatattactggaaacacaattctattagtccagcaaagcaccctagatgagaagtggcagatgatcatcaggtgtagtttcccattgttcactcattaacaggattctctatgatat-cagGTTGGTCTCAAGTACAATGAATCTGTGGTTATTCGGGTAACTGGCTGCCCTAATGGTTGTGCGAGACCTTACATGGCCGAACTTGGACTTGTCGGTGATG
upper sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ27223 (Selaginella moellendorffii), 3'ss of exon 4
gtattgctgcacatatatatggcagtattgatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaatt---cagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
||||||| | | | ||||| |||| || ||| ||| |||| ||||| ||| | || || |||| || | | || || || |||||||||||||| || ||||||||||| || |||||||| || || ||||
---------------------------gtgatttgtcttgttgtgtttcttgtg----ttaaatctttgctctctattattgcttagGTGGGCCTCAAGGAGGCGGATTCGATGGTGGTGCGAGTCACCGGGTGTCCTAATGGTTGTGCGAGGCCATACATGGCAGAACTTGGACTGGTCGGAGATG
upper sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ33435 (Selaginella moellendorffii), 3'ss of exon 6
gtattgctgcacatatatatggcagtattgatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
| ||| | ||| || | || | | ||| || | | | ||| | |||| ||||| ||| | || || |||| || | | || || || |||||||||||||| || ||||||||||| || |||||||| || || ||||
---------------------gtgatat-gtcttgttgtg--tttcttgtgttaaatctttgctctctattatttgc---ttagGTGGGCCTCAAGGAGGCGGATTCGATGGTGGTGCGAGTCACCGGGTGTCCTAATGGTTGTGCGAGGCCATACATGGCAGAACTTGGACTGGTCGGAGATGMapped 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|13311482|gb|BG405133.1|BG405133EST: AGCGTGGGATACCTAACATTCTTAAGCGGATTCGTGCTGTTTTTGATAAG GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AGCGTGGGATACCTAACATTCTTAAGCGGATTCGTGCTGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
cactaat putative branch site (score: 2)
cttttctgtct putative PPT
atacttaaaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgctgcacatatatatggcagtattgatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT