Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
Basic information
species | Glycine max |
transcript | GLYMA08G47680.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------gtaaaagcttctcttgttacc----tcactgtttgaacaattttctacggcattgactgattctt----tcgtgttt----cagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
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gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
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gtcagcaagattgtttgaaccctg--gttttgctagt---ccacgaaactaatcagctcttt-gcgcg-cagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------gtaaaagcttctcttgttacctcactgt--ttgaacaattttctacggcattgactgattctt----tcgtgttt-cagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
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gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtt-tcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
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gtagactgttcgaagatttgctca--gttggattggctcttttct-cagcggctgat-caaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
-gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
|| | || | || | || || | || | || || || | | ||||| ||| | || || ||||| |||| ||||||||| || |||||||| ||||||||||| ||||| || ||| |
gtcggtggcgtttcctcttctttttttgcttatgctgatt------gtgttataacgctcgtttgcg---cagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtt-tcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
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gtagactgttcgaagattttctca--gttggattgctcttttct--cagcggctgat-caaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
gactgat putative branch site (score: 3)
ttctttcgtgtttc CT-rich tract
aacaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG