Sequence
atgc intronic sequence ATGC exonic sequenceGTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggattccacctccttagctcaatgccatcgaattatttcgttctaggtcttgcgctcgtgaggtataatatatctctcctataaggtgaattgt...
Basic information
species | Physcomitrella patens |
transcript | PP1S431_6V6.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
------------GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagt--ggattccacctccttagctcaatgccatcgaattatttcgttctaggtcttgcgctcgtgaggt-ataatatatctctcctataaggtgaattgt
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TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa---
upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G113250_T01 (Zea mays), 5'ss of exon 2
------------GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggattccacctccttag-ctcaatgccatcgaattatttcgttctaggtcttgcgctcgtgaggtataatatatctctcctataaggtgaattgt---
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GGAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTTATTGCTCATGTGGACCATGgtaggttcagaacactgcccaagacattttgatgtc-aattgttctgtttcaatatttaagctt-tgtactgttcttgattgc--cgatgcttctattcatgct
upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AC203173.3_FGT004 (Zea mays), 5'ss of exon 1
---GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggattccacctccttagctcaatgccatcgaattatt--tcgttctaggtct-tgcgctcgtgaggtataatatatctctcctataaggtgaattgt
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ATGGTGAAGTTCACGGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAATATGTCTGTTATTGCTCATGTGGACCATGgtatgttcaaaacactacttt-gttagatgttatatagtccttaatatttttgagcctctttgtttttaaaatttatttcgttttcaatgtttaa-gagcta-
upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G095851_T01 (Zea mays), 5'ss of exon 2
------------GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagt--ggattccacctccttagctca-atgccatcgaattattt--cgttctaggtcttgcgctcgtgaggtataatatatctctcctataaggtgaattgt
|||||||| ||||||||||||| || || || |||||||| ||| ||||||| | |||||||| || || || |||||||| ||||||| || || | ||| |||| | || | ||| || |||| | | | ||| || | | || | | | | ||| |
GAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcagaacactgctctgtagcatatatatacatgcattgcttaacgttttcaagcctttttatgtg---tagacttaatttgctccaatatttgagct--
upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ28367 (Selaginella moellendorffii), 5'ss of exon 2
GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggattccacctccttagctcaat--gccatcgaattatttcgttctaggtcttgcgctcgtgaggtataatatatctctcctataaggtgaattgt
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GTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGgtgagtttcttctagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccag------------------------------------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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggattccacctccttagctcaatgccatcgaattatttcgttctaggtcttgcgctcgtgaggtataatatatctctcctataaggtgaattgt
- - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - AGAAGC