Sequence
atgc intronic sequence ATGC exonic sequencegtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
Basic information
species | Physcomitrella patens |
transcript | PP1S167_51V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
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------------------------------------------------------------------------------------------gctttcctttattgtttttatcacatatccgttaagtt-tctactggtggcatctctgttgt---------tagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 7
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
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------------------------------------------------------------------------------------------gctttcctttattgtttttatcacatattctttgagtt-tctactggtggcatctttgttgttagct--actgatagctatggttt-------tgttctatcacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACCCACTGCAATACGTTGGCATATAGTAGCTCTAAGGGATCCATTCGACTTGTTGATCTGCGCCAATCAGC
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 7
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttgg---ttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
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------------------------------------------------------------------------------------------------------------------------------------------gta-tagtcgcatctc--cggttcagtttttcatgtctgacaggatgatgttaacctttgtacagAAGTTATAACGTCTGCAGAGTTCCATCCCTCCCACTGCAATACTCTTGCTTATAGCAGCTCAAAGGGAACAATTCGTCTTATAGATATGCGGCAATCGGC
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 7
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
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-------------------------------------------------------------------------------------------------------------------------------------gtatagtcgcatctccgcttcagtttttcatgtctgacaggatgatg--ttaacctttgt---acagAAGTTATAACGTCTGCAGAGTTCCATCCCTCCCACTGCAATACTCTTGCTTATAGCAGCTCAAAGGGAACAATTCGTCTTATAGATATGCGGCAATCGGCMapped 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|100366505|gb|BY985168.1|BY985168EST: GAGTTTCAATATTGTTGACATCAAACCAACAAACATGGAAGACCTTACAG AGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCAT
genomic: GAGTTTCAATATTGTTGACATCAAACCAACAAACATGGAAGACCTTACAGgtattctctc ... ggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
gactaac putative branch site (score: 1)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG