Sequence
atgc intronic sequence ATGC exonic sequencegtctttacatcttcacccatttgtagatttcatactgaagtatgcgagtatcatattaaagttatcgagtcagtgaggtcatccaatcttatgaaaacgtcaaggtttcgagagcatttcgtaccatcctcttaaatagtcagtgatacgttgggcaataaaatggaccggaatgtgttctatttgatctataatacagATGGTCGCAGATAGCAACTCAGCTTCCCGGTCGCACAGATAACGAAATAAAGAACTTCTGGAATTCTTGCATTAAGAAGAAGTTACGAAATATCGGTATC
Basic information
species | Physcomitrella patens |
transcript | PP1S189_29V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G172327_T01 (Zea mays), 3'ss of exon 2
gtctttacatcttcacccatttgtagatttcatactgaagtatgcgagtatcatattaaagttatcgagtcagtgaggtcatccaatcttatgaaaacgtcaaggtttcgagagcatttcgtaccatcctcttaaatagtcagtgatacgttgggcaataaaatg---gaccggaatgtgttcta--tttgatctataatacagATGGTCGCAGATAGCAACTCAGCTTCCCGGTCGCACAGATAACGAAATAAAGAACTTCTGGAATTCTTGCATTAAGAAGAAGTTACGAAATATCGGTATC
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--------------------------------------------------------------------gtacgtacgggcatact-tcttgc-----cgtctatcttgct----ccctgctaactagtgactcaccggggccatggtgccatgcctcgtctggtctgtgcgcggcgcgcatgccaactccgatccaactcacagATGGGCGCAGATCGCCAAGCACCTGCCCGGGCGCACGGATAACGAGGTCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCATCGCGCAGGGCCTC
upper sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G57560.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctttacatcttcacccatttgtagatttcatactgaagtatgcgagtatcatattaaagttatcgagtcagtgaggtcatccaatcttatgaaaacgtcaaggtttcgagagcatttcgtaccatcctcttaaatagtcagtgatacgttgggcaataaaatggaccggaatgtgttctatttgatctataatacagATGGTCGCAGATAGCAACTCAGCTTCCCGGTCGCACAGATAACGAAATAAAGAACTTCTGGAATTCTTGCATTAAGAAGAAGTTACGAAATATCGGTATC
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------------------------------------------------------------------------------------------------------------------------gtaacaatcacaattacaattattctctgtttctgaaacagagtattttctgaaatcccctgtt--atcttgtat-cagATGGTCGCAAATTGCTGCGAGGCTTCCCGGGAGAACCGACAACGAGATAAAGAACTTGTGGAATTCGTGCATTAAGAAGAAGCTGATGAAGAAAGGCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatacgttgggcaataaaatggaccggaatgtgttctatttgatctataatacagATGGTCGCAGATAGCAACTCAGCTTCCCGGTCGCACAGATAACGAAATAAAGAACTTCTGGAATTCTTGCATTAAGAAGAAGTTACGAAATATCGGTATC
atttgat putative branch site (score: 5)
tatttgatctataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttacatcttcacccatttgtagatttcatactgaagtatgcgagtatcatattaaagttatcgagtcagtgaggtcatccaatcttatgaaaacgtcaaggtttcgagagcatttcgtaccatcctcttaaatagtcagtgatacgttgggcaataaaatggaccggaatgtgttctatttgatctataatacagATGGTCGCAGATAGCAACTCAGCTTCCCGGTCGCACAGATAACGAAATAAAGAACTTCTGGAATTCTTGCATTAAGAAGAAGTTACGAAATATCGGTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT