Sequence
atgc intronic sequence ATGC exonic sequenceCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg...
Basic information
species | Physcomitrella patens |
transcript | PP1S145_26V6.3 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 5'ss of exon 9
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg---
| |||||||| || ||||| || || || || ||||||||||||||||||||||||||||| ||||||||||||||||| ||| | || | |||| ||||| ||| |||| || || || | | || || || | || | | | || |
AGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAGgtacttgatcactgccttgactttt-aactcagaa--aattagaacctcgccaatcatcaagaaagcctcgttatagttagctgcctatggttgacaagaaag
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G097605_T01 (Zea mays), 5'ss of exon 9
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcc--tagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg
| ||||| || || ||||| || || |||||||| || ||||| |||||||| |||||||| ||||||||||||||||| || | || | | | | || | | | | | | | | | | | ||| ||| | | | | |
AGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAGgtacctgattactgccttaacgcacggagtcctagcatagctgagcatgaagcaacccacatcacatgcatagttgtatgctggcgaaccagctccagtc--
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA02G09080.1 (Glycine max), 5'ss of exon 10
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggt--ttcgttggg
| |||||||| ||||||||||| || ||||| ||||| || || ||||||||||||||||||||||| ||||| |||| | ||| || | ||| | | |||| | | | | || | | || | ||||| || | | | |||
AGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAGgt-tagtatcc-ttgtgcccttttgcttccatgaacacaatgcacatttgggaaaatgtgagggttgcttatggtattctacgctgacgttaagcaattgct
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA16G28290.1 (Glycine max), 5'ss of exon 10
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggt--ttcgttggg
| |||||||| || |||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| |||| | ||| || || ||| | | |||| | || | || | | || | | ||| || | | | || | ||
AGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAGgt-tagtatcc-ttgagtccttttgcttccatgaacatgttgaacatttgggaaaatgtgagggttgcttatagtattctacgctgacgttaatttgatgaa
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 5'ss of exon 10
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctc--tttccaactctgaataa--attttaagttcctagttctcgatgttttcca-agtggtacatgacttcaaaggtttcgttggg
| ||||||||||| |||||||| || || || ||||| || ||||||||||| ||||||||||| |||||||| |||| || ||| || || | ||| | | || || | | | | | ||| | | || | | | || | || | | | | |
AGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAGgtttgt-atcccttttatgtaaattttcctttttggatgagaaatccctctgacaagtgcacaattctgtatgcaaaggaaaataaatgtatatagtaaaa----
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: EFJ08988 (Selaginella moellendorffii), 5'ss of exon 9
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg
| |||||||| || || || || || || ||||| || ||||||||||| ||||||||||| ||||| |||||||||| | || |||| ||| |||| | | | |||| | ||| || | | || | || |
AGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAGgttttcc-cctgtcgtttctttttctttttttccttttctttt----ttctaatttt-gttgacattgaaacag--------------------------
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: EFJ30044 (Selaginella moellendorffii), 5'ss of exon 8
-----------------------CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg
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GCTTATTCGTTTACCTGTACCAGAGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAGgt-tatcccctgtcgtttctttttcttttttcc-----ttttcttttttctaatttt-gttgacattgaaacag--------------------------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|37830236|gb|BJ588248.1|BJ588248EST: GTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG GTACAATCGGCACGACAAGCGATCGAAACTACCTGGGTGGATTTTGTCACA
genomic: GTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatc ... catggaatagGTACAATCGGCACGACAAGCGATCGAAACTACCTGGGTGGATTTTGTCACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAGgtatgccatctgttccatctctttccaactctgaataaattttaagttcctagttctcgatgttttccaagtggtacatgacttcaaaggtttcgttggg
- - - - - - - - - - - - - - - - - - - - - GCAGAT