Sequence
atgc intronic sequence ATGC exonic sequence...attaggcgatggtttggcactaaactgggagcattttttgattttcgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT
Basic information
species | Glycine max |
transcript | GLYMA13G21320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G21320.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
---attaggcgatggtttggcactaaactgggagcattttttgattttcgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT-
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agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttatataccctttgtgtttctgaatttgttggt---tatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTG-AAGCAGATTGCCGATGGTGATCCTG
upper sequence: GLYMA13G21320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171987_T01 (Zea mays), 3'ss of exon 1
attaggcgatggtttggcactaaactgggagcattttttgattttcgaat-tttgttgactt--gttttgtttttgttgttttttgtg----tgtggagatct---gcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT-
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-----cccattgttcacga--aaattccga---ttttttcattccctgctatctagagattcagggagcatctgtcttgacgtttgtggaattgtcgatgttttgtgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGCGCTCAACACTACACAGAAGCAGCCATGGATGAGGTCAAGATCTTG-AAGCAGATTGCTGATGGTGATCCTG
upper sequence: GLYMA13G21320.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G53030.1 (Arabidopsis thaliana), 3'ss of exon 1
----------attaggcgatggtttggcactaa--actgggagcattttttgattttcgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT-
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gtacgcatctatctctctctctcgccacacgaattgcttgaaatgcttta-gagattaatttttcgttgctttgtttgtgtgattttcttactcgtatatcga-atgtacagAGATATGTGGCTTTGAAGGTGCAAAAGAGTGCTCAGCATTATACTGAAGCAGCCATGGATGAGATAACAATATTGCAA-CAGATTGCAGAGGGAGACACTG
upper sequence: GLYMA13G21320.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g04220.t01 (Vitis vinifera), 3'ss of exon 1
attaggcgatg-gtttggcactaaactgggagcattttttgattttcgaattttgttgac---ttgttttgtttttgttgttttttgtgtgtggagat-ctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT-
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---ttcctatgtgctcacgactaaat--ggagtgttattagggaataatgtttttttaataaatttctttgtattaaataataacataattggcatatgctgcagCGGTATGTGGCTCTGAAAGTTCAAAAGAGTGCTCAGCATTACACTGAAGCAGCTATGGATGAGATAACTATATTGCAA-CAGATTGCGGAAGGAGACCCAGMapped 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|209721194|gb|BW665725.1|BW665725EST: GTTGGGGCCATTTCTCCACTGTCTGGCTCGCTTGGGACACCAAACATTCT AGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCG
genomic: GTTGGGGCCATTTCTCCACTGTCTGGCTCGCTTGGGACACCAAACATTCTgtctgttcct ... agatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT
tgttgac putative branch site (score: 3)
tttttgttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaggcgatggtttggcactaaactgggagcattttttgattttcgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg