Sequence
atgc intronic sequence ATGC exonic sequence...actggactttatgtatgaatctgcctgtgaatcatagttatttgttggtaaatcggcattctctctgtattttcttagaacgttctgttggtgtctatagGTTGCTGTATTACAAGACATCAACAAGCGACTACAGGAGTACAACACAAGTTTACAGCAATATAATAGTAAATTACAAGTGGATGCCAGTAATGCCGCTG
Basic information
species | Physcomitrella patens |
transcript | PP1S80_62V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S80_62V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------actggactttatgtatgaatctgcct-gtgaatcatagttatttgttggtaaatcggcattctctctgta---ttttcttagaacgttctgttggtgtctatagGTTGCTGTATTACAAGACATCAACAAGCGACTACAGGAGTACAACACAAGTTTACAGCAATATAATAGTAAATTACAAGTGGATGCCAGTAATGCCGCTG
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gtaatagaatttataaagatcttattagcagttgc-tagaatcctgttttgtttgttctcatttccaattagtactgtaaaaccaccttagcaaatctttttcatcccgaactgttgaattctgcagATAACATCTCTTAATGATATGTACAAGAGATTACAAGAGTACAACACAAGTTTACAGCAATACAATAGTAAACTTCAGACAGAGCTTCCCACAGTGAATG
upper sequence: PP1S80_62V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 5
actggactttatgtatgaatctgcctgtgaatcatagttattt--gttggtaaatcggcattctctctgtattttcttagaacgttctgttggtgtctatagGTTGCTGTATTACAAGACATCAACAAGCGACTACAGGAGTACAACACAAGTTTACAGCAATATAATAGTAAATTACAAGTGGATGCCAGTAATGCCGCTG
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-------gtaatgtaacaacagtcatctagatgatttgtgtttttatctccgaattcatataattaatgt-ctccctttgtatatt---ttgaattttgcagGTAACCTCACTAAATGATATGTACAAGCGATTGCAAGAGTACAACACAAGTTTACAGCAGTACAATAGCAAGCTTCAAACAGATCTTGCAACGGCAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtaaatcggcattctctctgtattttcttagaacgttctgttggtgtctatagGTTGCTGTATTACAAGACATCAACAAGCGACTACAGGAGTACAACACAAGTTTACAGCAATATAATAGTAAATTACAAGTGGATGCCAGTAATGCCGCTG
tattttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actggactttatgtatgaatctgcctgtgaatcatagttatttgttggtaaatcggcattctctctgtattttcttagaacgttctgttggtgtctatagGTTGCTGTATTACAAGACATCAACAAGCGACTACAGGAGTACAACACAAGTTTACAGCAATATAATAGTAAATTACAAGTGGATGCCAGTAATGCCGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA