Sequence
atgc intronic sequence ATGC exonic sequenceCTACCCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTGGTTTCCGCAGGTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttccttattgatgatagacttcattttttccattgtgagcagagtattcatgaatttttgtatcttcggttgtgagaatttt...
Basic information
species | Physcomitrella patens |
transcript | PP1S3_334V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S3_334V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os01g05490.2 (Oryza sativa), 5'ss of exon 1
CTACCCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTGGTTTCCGCAGGTTTCAG--GATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttcctt---attgatgatagacttcattttttccattgtgag-cagagtattcatgaatttttgtatcttcggttgtgagaatttt
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-CTCTTCCCCCCCCCCCCCCCCCCCCCCGCGTCCAGTTCCATCTAATCAGCTTCTCGTCGAGATGGGC-CGCAAGTTCTTCGTTGGTGGCAACTGGAAATGCgt-aatttttttctcttcctgcttgaaatctctagtcgcatgttcttgtgtctcggtgactcaggagaatttttgattttt---ttttctgttctggaacgcga
upper sequence: PP1S3_334V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G018177_T02 (Zea mays), 5'ss of exon 1
CTACCCGTCACCGATTTGACCATCCCGCTTCTCCA-GTGTGGTTTCCGCAGGTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttccttattgatgatagacttcatttt--ttccattgtgagcagagtattcatgaatttttgtatcttcggttg-tgagaatttt
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TGGGCCGCAAGTTCTTCGTTGGTGGCAACTGGAAATGCGTAATTTCTCTTCCCCCGTCGAACTGCCTATTTT--TCTTTCGTGGATGGGATGTGGACCTTTGgtagtatatctgatcccgtttacggttaagctaggcagtgttttgtttttgtttttgtttttgt-ttggggagggggtttggattcgattgctctggattc-
upper sequence: PP1S3_334V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G018177_T01 (Zea mays), 5'ss of exon 1
-------CTACCCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTGGTTTCCGCAGGTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttccttattgatgatagacttcattttttccattgtgagcagagtattcatgaatttttgtatcttcggttgtgagaatttt------
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TTTAGAAGCGCCCTTCCTCCTCTCCCCCATCCG---TACCCAATCTAATCGACACCCGGC-CGAGATGGGC---CGCAAGTTCTTCGTTGGTGGCAACTGGAAATGCgtaatttctctt--cccccgtcgaactgcctat---ttttctttcgtggatgggatgtggacctttggt-agtatatctgatcccgtttacggttaagctaggcag
upper sequence: PP1S3_334V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 1
--CTAC-CCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTGGTTTCCGCAGGTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttccttattgatgatagacttcattttttccattgtgagcagagtattcatgaatttttgt----atcttcggttgtgagaatttt-----------
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AACTCCACTGTCTCCAACTCT-CCATCGCG--TCTGCTACGCCTCTCCTGCAGGACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtccccctaggacccaggctccaggcacca----ccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctctgatggcatccgctcccccgtgtgcag
upper sequence: PP1S3_334V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA15G04290.2 (Glycine max), 5'ss of exon 1
CTACCCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTG----GTTTCCGCAGGTTTCAGGATGTGTTCGCGG-----AAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcat-gtccccttccttattgatgatagacttcattttttccattgtgagcagagtattcatgaatttttgtatcttcggttgtgagaatttt--
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--------CAAGGGTTTCTCTGTCT-GCTTCTTCACTTTCTCTCGTTTCAATCGAAACCAAAACAAAATCATGGGCAGAAAATTCTTCGTTGGTGGCAACTGGAAATGCgtatgtttcaatcactatcttctccacttaccttt--ctttttttgtttctgtgaatttgttttaatctcga-tgaatgaaatctcggtagttctactctacaMapped 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|18350897|gb|BJ182948.1|BJ182948EST: GTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGC AATGGAACCGTTGATGAGGTGAAGAAAATATGCTGTATGCTAAACAATGGA
genomic: GTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttc ... attgttacagAATGGAACCGTTGATGAGGTGAAGAAAATATGCTGTATGCTAAACAATGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTACCCGTCACCGATTTGACCATCCCGCTTCTCCAGTGTGGTTTCCGCAGGTTTCAGGATGTGTTCGCGGAAGTTTTTCGTTGGTGGCAACTGGAAATGCgtcagtcttcatgtccccttccttattgatgatagacttcattttttccattgtgagcagagtattcatgaatttttgtatcttcggttgtgagaatttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG