Sequence
atgc intronic sequence ATGC exonic sequencegtaaggagtttgtttgctattgattcgtttcttcgctggtagctaacgggtttgttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ17248 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 2
-------gtaaggagtttgt--ttgctattgattcgtttcttcgctggtagctaacgggtttgttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
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gtaattcattggaagcttgtaatggtggttggctgatggcaacgtgaaattgtgctgagttggattttgttttttggttgcagGCATGATCGAGCCAAGGCGGTGGAGATACTCGTGAAGGATCTCAAGGTGTTTGCCTCATTCAATGAGGAGCTGTTCAAGGAGATAACACAGCTGCTGACG
upper sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030422_T04 (Zea mays), 3'ss of exon 4
------gtaaggagtttgtttgctattgatt-cgtttcttcgctgg--tagctaacgggtttg---ttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
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gtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
upper sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtaaggagtttgtttgctattg--attcgtttcttcgc-tggtagctaacgggtttgttacctc--tctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
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atgcattgtttgatttagaaatctgagtatttaattttttttttgcatttgttcatgtgtatggtatttgataa-tctgttgttttgattcttgttatcagGCAGGACCGAGCAAAGGCTGTTGAGATTCTTGTCAAAGACCTTAAGGTTTTTGCATCTTTCAATGAAGAGCTATTTAAGGAAATTACCCAATTGCTTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattcgtttcttcgctggtagctaacgggtttgttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
agctaac putative branch site (score: 2)
tttgttacctctctct putative PPT
tttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggagtttgtttgctattgattcgtttcttcgctggtagctaacgggtttgttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA