Sequence
atgc intronic sequence ATGC exonic sequencegttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
Basic information
species | Glycine max |
transcript | GLYMA06G47850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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-------------------gttagtttttttcttgtgt-gtgttgctttttcca---taaataatt---tttgttaagacttaacgttagtacgtttgattta---aagACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaat-taattgattgact-tggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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-----------------------------------------gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctt-tgc-tgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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--------------------gtatgtgtttaggccacttgatctgtaatctatctatgtgat-atgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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gtctgtgcttaagtttgattctgcaaataattttttttttttttg--tcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
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--------------gttcgacttgctcttcttttttttttaatca-tatttc---acctatc-accaactggggtaact---gaattattttttcttgtttc---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|8670223|gb|BE191330.1|BE191330EST: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGTTATACTATTGAG ACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCA
genomic: TAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGTTATACTATTGAGgttggatttt ... tttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
cttggattcccttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT