Sequence
atgc intronic sequence ATGC exonic sequence...ctatcatgaatgtcattgtttgtgatctttctatattattcccaatttcccatcaactaacgctgtcatcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
Basic information
species | Glycine max |
transcript | GLYMA02G44810.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 1
ctatcatgaatgtcattgtttgtgat-ctttctatattattccca-atttcccatcaactaacgctgtcatcaaaatttatatcct--cttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
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----cgcaactatttgcgccgaaatcactttgcagagtatacatacatgatcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
upper sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 1
ctatcatgaatgtcattgtttgtgatctttctatattattcccaatttcccatcaactaacgctgtcatcaaaatttatatcctcttat----ttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
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gtaagaaccccgagtttgttcatgttttgcaaacgccattag-atggcaaaatcatttcgtgaagttaaaacgagctct-tgctgatatgacgttcctacgcagGGTTACATTGTCCTAAACAGGCCTTGGGCATTTGTTCAATGGCTGAAGAAATCAAACATCAAAGAAGA
upper sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 2
ctatcatgaatgtcattgtttgtgatctttctatattattcccaatttcccatcaactaacgctgtca--tcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
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---------gtgaggttttggttggtccttttgtggtgttt---gtttccagttta-tgatggtaccaccttgtgctcttgctgatatgatgatttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAAGCAAAGATCGTAGAAGA
upper sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 1
ctatc-atgaatgtcat-tgtttgtgatcttt-ctatattattcccaatttcccatcaactaacgctgtcatcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
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taatctgttgatgtcacgtgattgaagtatctattccactgatttgcttgtctgacgtcttgatg--gtctgtacaactgacattccaatgttcttt-tgcagGGATATGTGGTCCTAAATAGGCCGTGGGCATTTGTGCAGTGGCTTCAGAAAGCAAAGATTGAAGAAGA
upper sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 1
---ctatcatgaatgtcattgtttgt--gatctttctatattattcccaatttcccatcaactaacgc-tgtcatcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
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tttcctttttaaatttgtttagacattggatttcattagatgat----aacttctaa--aatcaatatgtatccttattctcattgtattcaaatgttgtacccagGGATACATTGTCTTAAATAGACCATGGGCATTTGTGCAATGGCTGGAAAAAGCTACGATTGAGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcccatcaactaacgctgtcatcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
aactaac putative branch site (score: 1)
tatcctcttattttt putative PPT
aaaatttatatcctct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatcatgaatgtcattgtttgtgatctttctatattattcccaatttcccatcaactaacgctgtcatcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA