Sequence
atgc intronic sequence ATGC exonic sequence...ctctagctcttattttttatgaccctattttgaattgtgtttttattttattttttggttacatgtctggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
Basic information
species | Glycine max |
transcript | GLYMA05G26240.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
ctctagctcttattttttatgaccctattttga-attgtgtttttattttattttttggttacatgtctggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
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gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaatgttaaatgatggcat-tctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------------ctctagctcttattttttatgaccctattttgaattgtgtttttattttattttttg---gttacatgtctggtggt-ttaata------tttgaaactttt-----aaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
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gtttttaccttgctttatttatatttttttatttcatctcccattcttccatcattccgttgcaagtgaaccagcattggactatc-taatcaaaatacaagtattgtgataataaacttgcttgaatggtgcttgccttctggggttaatgacatcttttgcaacattctgttgaaaactagGTAGCAAGGGCTCCTGATGGCAATGGTGGAGTGTATGCTG
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 6
ctctagctcttattttttatgaccctattttgaattgtgtttttattttattt--tttggttacatgtc-tggtggtttaatatttgaaacttt---taaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
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------ttttcattttgacagagtcttttttttaatatatactgagcaaaaaaaaacaaatgctaagttgtggcattcttgttgtccatgctgtggatgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 7
ctctagctcttattttttatgaccctattttgaattgtgttttt---attttattttttggttacatgtctggtggtttaatatttgaaactt-ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
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--taggattatttccatttttaccctcctt--agctgaattttttaaatttcaaatttgttctgaaaatatagtggttacatatatctaatttcttaaagccagGTAGCTAAGGCTCCAGATGGAAATGGAGGAGTATATTCAGMapped 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|7924327|gb|AW830353.1|AW830353EST: TCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGG GTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
genomic: TCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGGgtatactctc ... ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
EST:
gi|254346278|gb|GR859891.1|GR859891EST: TCCCTTGTGTTTCCA-GGATGGTAGATTTATTATGGAGACTCCATACAGG GTAGCAA-GGCTCCTGATGGGAATGGTGG
genomic: TCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGGgtatactctc ... ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattttttggttacatgtctggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
gtttaat putative branch site (score: 4)
ctttt putative PPT
tttaatatttgaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctagctcttattttttatgaccctattttgaattgtgtttttattttattttttggttacatgtctggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - atgaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggt