Sequence
atgc intronic sequence ATGC exonic sequence...taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
Basic information
species | Glycine max |
transcript | GLYMA19G38720.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g34000.1 (Oryza sativa), 3'ss of exon 6
taaatgcacattcacctacacatgattctttctcatgctttacatacccagactc--catctggaacttgttttgattaaatttggttcttattt--attgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
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---gtgagtat-cattttagcaagctgctaaaatgaaccct-cattctctggcttatcatttactatttattgacaatggccttttttcttttcttaattttagGTATAAGGTTTTCATTAATCCAAGTGTCAGTGATGTTCTATGCACAGCGACAGCTGAGGCTCTTGCAATGGGGAAATTTGTTATCTGTGCAGATCATCCA
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
--taaatgcacattcacctac-acatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
||| || | | | || | ||| ||| | || || | | | || || | |||||| || || || ||| || |||||||| || ||||||||||| |||||||| ||||| || ||||| || || ||||||||| | || ||||| || ||||| || || || || || |||
gtaaaagacagagcctctcactgcctgacatcttcctacatctt---tagatatagttaatttgaa---tgttttt------cctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: AC233887.1_FGT006 (Zea mays), 3'ss of exon 6
-------taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctgga--acttgttttgat-taaatttggttcttatttattgt-agGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| | | | ||| || | | | ||| || | | | | || | || || | | | ||| |||| | ||| | |||||||| || ||| | ||||| || |||| ||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||||| |||||||||
gtgaggttctacgaagcatcaaagctac-taaaacgacatcacttttatcttgatcttgtcctatgcaaattgctgattcaggtatctgttttcttctgttgaattttcagGTACAAGGTTTTTGTCAATCCAAGTGTTAGTGATGTGCTATGCACAGCAACAGCTGAGGCCCTTGCAATGGGGAAATTTGTAGTCTGTGCAGATCATCCA
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| | ||| | | || || | | | || | || | | ||||||| ||| | | || || ||||||||||| || ||||| |||||||| |||||||| ||||||||||| || || || ||||| |||||||| || ||||| || ||||| ||||| ||
-----gtaagttctgaaaaatgtgctttgcttttaaa---aacttgttaaggtttcgctc---------tttgattgtctttcccacat-cttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
upper sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 6
--taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctggaacttgtt--ttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
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gactgaaatatttctcctggggaataatgtagttccata---taaatgatt-gtgaacaaatgaaccttgctgattgttgtcacatctttctttttccttgcagTTACAAAGTCTTCATAAATCCCAGTGTCAGTGATGTGCTCTGCACAGCTACAGCTGAGGCCCTTGCTATGGGTAAGTTTGTAATATGTGCAGACCACCCAMapped 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|19348880|gb|BM893412.1|BM893412EST: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCACAG GTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTAC
genomic: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCACAGgtaggtacac ... tttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTAC
EST:
gi|6963802|gb|AW432495.1|AW432495EST: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCACAG GTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTAC
genomic: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCACAGgtaggtacac ... tttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
ttttgat putative branch site (score: 4)
ttcttattt putative PPT
ttttgattaaatttgg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- aatgcac
- - - - - - - -ctacaca
- - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - cataccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg