Sequence
atgc intronic sequence ATGC exonic sequencegttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
Basic information
species | Glycine max |
transcript | GLYMA04G12890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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-------------------gttagtttttttcttgtgtgtgttgctttttccataaataatt--tttgttaagacttaacgttagtacgtt-----tgattta---aagACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT
upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctc--cctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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-----------------------------------------gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccc-tcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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--------------------gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
-gttgggtttta--tgacttctgctatcccttttcacattttaaatcactgtttct-caatt-aattgattcacttggattcccttctctctccctcctca---tgctttgc--tgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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--------------gttcgacttgctcttcttttttttttaatcatatttcacctatca------ccaactggggtaactgaattattttttct--tgtttc---aaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATMapped 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|15203210|gb|BI425978.1|BI425978EST: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGCTATACTATTGAG ACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCA
genomic: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGCTATACTATTGAGgttgggtttt ... tttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCA
EST:
gi|23727557|gb|BU761813.1|BU761813EST: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGCTATACTATTGAG ACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCA
genomic: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGCTATACTATTGAGgttgggtttt ... tttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
cttggattcccttctc CT-rich tract
attgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT