Sequence
atgc intronic sequence ATGC exonic sequenceGGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgcttacaaagattttctttgcacag
Basic information
species | Physcomitrella patens |
transcript | PP1S141_116V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S141_116V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
GGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgctta---caaagattttctttgcacag
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------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTC--GAGTGGTCAGCATGTGGAATGTA----------TCAGGTCCAC----TGATTCAGAGgtgcaa---cagctttg---ttgattttttccacagacaaatttctctcttgtgacaaaattctaattagttattgctttttggctcatag---------------
upper sequence: PP1S141_116V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
GGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGA---ACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgcttacaaagattttctttgcacag
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---ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaa-------tttaaatgttttacttgctttcttagtgtgtatc-ttcttatcctcctcgtag-------------------------------------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|100387739|gb|BY951739.1|BY951739EST: AAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAG GGTAATGATGTTGTATTCTTCCAGCCTGCAAGCGAATACCTTCCAATGATG
genomic: AAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtgagttcca ... ctttgcacagGGTAATGATGTTGTATTCTTCCAGCCTGCAAGCGAATACCTTCCAATGATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgcttacaaagattttctttgcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG