Sequence
atgc intronic sequence ATGC exonic sequencegtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA07G04260.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g07940.1 (Oryza sativa), 3'ss of exon 2
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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---------------------------gttggtgacgacattgct-gcttctccattgcttccggcgtgtctcactgatccatgtctacgtg-ctcatcatttttttcagACATAGATGGACTGGAAGATACGAGGCTCACTTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACCAGGAAAGGAAGGCAAG
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g01370.t01 (Vitis vinifera), 3'ss of exon 3
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgtt--agGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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-------------------------gtattgaaagaaacaaattttaattcttt-tcttttcttttctttgaagagaaaattttgatgggtgggtgatgaaatttgttttagGCACAGATGGACTGGAAGATATGAAGCCCATTTGTGGGACAACAGTTGCAGAAAAGAAGGACAAACAAGGAAAGGAAGGCAAG
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaggagtaatagattttaatgttttttt--taattgttgca-tggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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----gggtg-tagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgt------ttgattt--gtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggagtaatagattttaatgttttttt--taattgttgca-tggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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---ggcgcag-agagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtatt-------gtgtgttgatttg--tagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgcttt-gtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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-----------------------------------gtacgtgatcgacaacttttgatcgatatatggaggaaccatagctagactaatcacgggttt--gatggagC-AGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
upper sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 2
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgcttt-gtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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-----------------------------------gtacgtgatcgacaacttttgatcgatatatagaggaaccatagctagtctaatcacgggttt--gatggagC-AGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
ttttgat putative branch site (score: 4)
ttttgtt putative PPT
ttttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA