Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
Basic information
species | Glycine max |
transcript | GLYMA07G39380.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gtttgtgc-ctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaat--actgggtccatcaactcaattttt-------tgatt-tgctatgatatt-------ttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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gtatgcacactatagttccctgtcacttgttggatacccagattggaa----cctaagaacgggctttgtggaagtgatgtt-tgcagcatgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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-------------------------------acctacagtattaggagcatctgggagatgtcttatattg--tgattgtggctgatcgtatgtacttgcat--gatttggtcgctgtctttttt--------------ctttgcttagGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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-----------------------------------acagtgttaggaatacctgggagatatcttataatg--tgtttgtgactgatcttat------gtacttgcatgatttaatcgctgtctttttttttt------cttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctaga--ttggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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---------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataat----agcctttggtaa-actag---tatgtgcttagaatga-gatgagttaacttattg-gcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
--------------------gtttgtgcctatgctcttcacattatcttctaatcatcaaatta----gatatttcttctagatt---ggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttt-tgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggtt--atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGMapped 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|26058870|gb|CA801784.1|CA801784EST: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
ttttgat putative branch site (score: 4)
tcaattttttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
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