Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtggattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S65_90V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S65_90V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtg-gattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
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----------------------------------------------gtgcaagcatataattgtccccttgttatatttttaattctc-caagggtgaccaggggggac-cagaatgctaactaagcattcct---tgtctgtcttca-cagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
upper sequence: PP1S65_90V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv10s0003g02590.t01 (Vitis vinifera), 3'ss of exon 9
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtggattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
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----------------------------------------agaacacagctttcatg--tcaaaatgaatgtttgttatttgtgatatgaaaggtacagttt--aattgttc-attgctctttaaacttcatatctatt---gctt---agGTGAGCCATACAGGATGGTCAGAAGGAGAATGCAAAGGTAAAGCAGGCTGGTTTCCATCAGAGTACGTGGCAAAACGTCAAAGGCTTCCCACCAGTAATG
upper sequence: PP1S65_90V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ27680 (Selaginella moellendorffii), 3'ss of exon 8
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtggattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtgg-aaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
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------------------------------------------------------------------------------------------------------gtgggtgacgagccaaagtcattgaatgaatgaacgtttttcttttgcagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG
upper sequence: PP1S65_90V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ37265 (Selaginella moellendorffii), 3'ss of exon 8
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtggattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtgg-aaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
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------------------------------------------------------------------------------------------------------gtgggtgacgagccaaagtcattgaatgaatgaacgtttttctttggcagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
aactaat putative branch site (score: 2)
taatagatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtggattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG