Sequence
atgc intronic sequence ATGC exonic sequence...tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
Basic information
species | Glycine max |
transcript | GLYMA20G19980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatt---tcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
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-----------------------gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 6
-tcatttctttttctgccattatccctaattccaacttagttttaattttttcccct-tgtattctgtatcttacagtgcctgatcattgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
| | | | | || | | | || | | | | || | || | || | | | ||| || || | || ||||| || ||||| | | |||||||||||| ||||| || || |||||||||||||| || || || ||||| |||||||| || || ||||| || |
ttgaaataagataccaat-ttgtgcattatacgcctcaggatatgatagataagtgaatgcaaccta-gtgctcccgtgatggacggttacgttccttgcagGACGGAAAAACTCTGTTTAATGAGTTGGAGGTTGTGGAGGGTATGAAGCTCGACAGAGGATATATCTCTCCCTATTTCATCACCAATTCTAAGACTCAAA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 6
-tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcc-tgatcat-tgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
|| | | | | || | || | | | || | |||| || ||| || | ||||| | |||| || | || |||||||| || || |||| |||||||||||| ||||| || || |||||||| |||||||| || || || || |||||||| || || | |||| |||||
cccacaaggtctccattc--tagcattatgtgccagagggtatagatttcgattaaatgccatcta-atggtccagtgatgttctcatgtggtattatcacagGATGGAAAGACTTTATTTAATGAGTTGGAGGTTGTGGAGGGCATGAAGCTTGACAGGGGATATATTTCCCCCTATTTCATCACTAATGCAAAGACCCAGA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
| |||| || |||| | | | | ||| ||| | | || | | ||| | ||| ||||||| |||||| | | ||||| || |||||||| ||||| |||||||| |||||||| || || || ||||||||||| || ||| | || | ||||
gtaagtgggaaatacatttgaacatgttggtctgcgatgtcattgtggttcattgtcattaaatgggcctggtatcaaaaattggagttaatctgcacatgtttcctcccttatgtttgacct---ttcacccataaatttctttaagtcagcatgagatgagaactcattaaaccatgaaattgtttttagGATGGTAAAACACTTTTCAATGAATTAGAAGTTGTGGAAGGCATGAAGCTTGACAGGGGTTATATCTCACCTTATTTCATCACCAACAACAAAACTCAGAMapped 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|193364498|gb|FK333539.1|FK333539EST: GGCAAAGAGGGAGTAATCACAATTTCA GATGGCAAAACCTTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTC
genomic: GGCAAAGAGGGAGTAATCACAATTTCAgtaagttttt ... accatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTC
EST:
gi|19269094|gb|BM885350.1|BM885350EST: TTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA GATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTC
genomic: TTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagttttt ... accatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
ttgtaac putative branch site (score: 2)
ccatttc CT-rich tract
ttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatttcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - ctgccat
- - - - - - - - - - - - - - -tccaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcctg