Sequence
atgc intronic sequence ATGC exonic sequence...catatgacgcatgagtttaatgggggtgagtggtgggaatgtggcagggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA
Basic information
species | Physcomitrella patens |
transcript | PP1S431_6V6.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S431_6V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------------catatg-acgcatgagtttaatgggggtgagtggtgggaatgtggcagggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA
|| || | ||| | | ||||| || | ||| ||||| |||||||||||||| || || || ||||||||||| || || || || ||||||||||| |||||| || ||||| |||||||||| || ||| |||||
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttgggg-tggg-ggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC-----------------------------------------------------
upper sequence: PP1S431_6V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20382 (Selaginella moellendorffii), 3'ss of exon 2
------------catatgacgcatgagtttaatgg----gggtgagtggtgggaa---tgtggcagggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA
| || ||| || | | | | | | | ||| | | |||| || || || ||||||||||| ||||| || || || ||||||||||| |||||| ||| ||||| || || |||| ||||| || |||||||||||
gtgagtttcttctagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccagGAAAATCCACCCTGACGGATTCCCTGGTTGCGGCCGCTGGGATTATCGCCCAGGAGGTGGCTGGAGACGTCCGGATGACCGACACACGCCAGGATGAGGC-----------------------------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|18353865|gb|BJ185920.1|BJ185920EST: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG GAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGAT
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... tatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA
cactgac putative branch site (score: 2)
attat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatgacgcatgagtttaatgggggtgagtggtgggaatgtggcagggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgcg