Sequence
atgc intronic sequence ATGC exonic sequence...aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
Basic information
species | Physcomitrella patens |
transcript | PP1S326_37V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g37970.1 (Oryza sativa), 3'ss of exon 1
--aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| ||| | | | ||| | || | | | | || | | ||| | | | | | || || || | | |||| | ||||| ||||||||||| |||||||||||||||||||| ||||| || ||||||||| | || ||||| || |||||||| |||| ||
tcgaaaagcactca--tttgcacaatgattgtagaatttaacacctgatatctgaatcttctgctgatctagcctgatcaatgaacaccttgtgattcgcagGTTTGAACAGGTGTGGCAAGAGCTGCAGGCTGCGGTGGACGAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCTCCCAGGAGGAGGAGCAGACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 1
------------------------------aatgggcagtgagatca-----atggaattgagtcatgtttcag----ggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcatttttt---ttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
|||| | || | | ||| || ||| | | || |||| | ||| || | | |||||| | | | | | ||||||| |||||||||||||||| ||||||||||||||||||| ||| | || ||||||||||| || | ||| | | |||||| || || ||
gtacgtacgttcgtctcttttgcgatcgatctggggccgccgcgtcgcgcgcgcgtggtccagtagtgcttccgtttcgttttttttgtgcggttttcg-ctg-aggcgaggcgcgtgtgcgcgatcgatgggtgcgtgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTGCGGCCGGACATCAAGCGCGGGCCTTTCACCCCGGAGGAGCACAAGTCCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 1
---aatgggca-gtgagatc------aatggaattga--gtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttcttt---cagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| | || || || | | ||||| |||| | | | || || || | | | | | | || || ||| ||| ||||||| |||||||||| |||||||| ||||||||||||||||||| || || || ||||||||||| || || ||||| ||||||||| || ||
gtgagcgcgcgcgtcagctttgctctgccgccattgatgagcatgcacaaagctagcttagattagcttatcttatgaatggtaactgatatatccagcttctttgtttgtgcagGGCTCTCGAGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGTGGTCGCTTCTCCTTCGAGGAGGAGGAGGCCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 1
aatgggcagtgagatca-atggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
||||| | | || ||| | || | || | || | | | | |||| | | || |||| | ||||||||||||||| || ||| |||| ||||| ||||| |||||||| ||||||||| ||||| |||| | || || |||| ||
--------gtgagtttggacagacctgaatttcaccctcttgcaaagaaatgtaggtaaaatgctatgaaatttagtgagaatttggtcaacatattgcagGTTTGCAGAGGTGCGGCAAGAGTTGCAGGTTGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
--aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
||| || | | | | || || |||| | | || | | | | || | | | || || || | | ||||||| |||||||||||||||| ||||||||||||||||||| || | || ||||||||||| || | ||| | ||||||| | || ||
ctctcttttcgtgc-atgagaagtactcggt-attattcacaggagctgagagactctagtccgttccatctggataacacttcgttttgcgttgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 1
-------------aatgggcagtgagatcaatggaattgag-tcatgtttcagggcga-caaagtagagtttctgtctgcagtcc--cattctgagtgcgcattttttttc----tttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| || | | | |||| | | | ||| | || | || | | | | || ||||| | |||||||| || ||||||| ||||| ||||||||||| ||||| | ||||||||||| ||||| || ||||||||| ||||| ||| | | ||| | | | ||
gtatgtgtacatgcacaacggatggcgtacgtagctttgatcttgtagctagcatcgatccaaatgcagctatagctcgatggccatggcgttgagttttccttttttttacatgttgcagGGCTGAACAGGTGTGGCAAGAGCTGCAGGCTAAGATGGACGAACTACCTGAGGCCAGACATCAAGAGAGGAAAGTTCACCTCTGCCGAGAAGGATACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 1
-----aatgggcagtgagatcaatggaattgagtcatgtt------tcagggcgacaaagtag------agtttctgtctgcagtcccattctg----agtgcgcattttttttct---ttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| || || |||| | | | || | | || | | | || || ||| || || || | |||| | || | ||||||||| | |||||||||||||||| |||| |||||||||||||| || | || ||||||||| | || ||| | | ||||||| |||| ||
gtacgtgcgtgccatgcgatctcggttttcggcctctgataactagctaaatcgcctgatcgatccgccaattgctcactggtgtggttttttgggggaatgcgtgtgttgacgcataattcagGGCTGCGGCGGTGCGGCAAGAGCTGCCGGCTCCGGTGGACGAACTACCTTCGGCCGGACATCAAGAGGGGCAAGTTCACGCTGCAGGAGGAGCAGACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G110135_T01 (Zea mays), 3'ss of exon 1
--------------------aatgggcagtgagatcaatgga--attgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| | || |||| | | || | | | | || | | | | | | || | | | | | ||||||| ||||||||||||||||| ||||||||||||| ||||| ||| | || ||||||||||| || ||||| | |||||||| |||| ||
gtacatgcatgcatgcatgcccttctccgtccgatcgtctgtctgtctagctgtagctttgtatggattagctagctgatcagcgatggaggagctagctgaacatatatatatgcatgcagGGCTGAACAGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACCAACTACCTGCGGCCGGACATCAAGCGGGGCAAGTTCTCGCGGGAGGAGGAGCAGACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G031323_T01 (Zea mays), 3'ss of exon 1
---aatgg-gcagtgagatcaatggaatt---gagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcatttttttt--ctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| | || ||| | | |||| | | |||| || | | ||| || || || | | | || | | | ||||||| || ||||||| |||||||| |||| |||||||| ||||||||||| || ||||||||||| || || ||||| ||| ||||| ||| ||
gtgagcgccgccctgaccccgacggaactctcgtcccatgaatcctacgcatatagtgtagacatattcatgcatctcgtgacacatcgatccttctcgtgacacacagGGCTCGCACGGTGCGGGAAGAGCTGCCGGCTACGGTGGACTAACTATCTGAGGCCGGACATCAAGCGCGGCCGCTTCTCCTTCGACGAGGAGGAGACAAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G123202_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------aatgg-gca-gtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgc-gcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
|| ||| | | || | | | | || || | || || | || | | | | || |||| || | | | ||||||| |||||||||||||||| ||||||||||||| ||||| ||| | || ||||||||||| || | ||| | | ||||||| || | ||
gtacgtacgtacgtgctctgttcctcggtcgagcccagcccgggccgcctggtgctgcatgcgtgacctagttgttcgcctcgtgctcgtcatttcttgagc-gactcgtggtgtaaaatgcgatgtgatgtgccgcgcgcgcatgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACCAACTACCTGCGCCCGGACATCAAGCGCGGGCACTTCACCCCCGAGGAGCACAACTCTAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G166337_T01 (Zea mays), 3'ss of exon 2
aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttcttt-cagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
|| || ||| || | || | | | | | || | || || | | | | | || | ||||||| || ||||||| |||||||| ||||||||||||| ||||| ||||| || ||||||||||| || || ||||| ||||||||| || ||
-gtgagcgagcgacctgctggccccgatcgacgtc----gatcatgcgcatatatacacatatccatgctcacctcgatcgtccttctcatgtcatggcagGGCTCGCACGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACTAACTACCTGAGGCCGGACATCAAGCGCGGCCGCTTCTCCTTCGAGGAGGAGGAGGCTAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------aatgggcagtgagatcaatg-gaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcatttttt---ttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| | | | | || | || | || | | || | | || ||| ||| | | |||| || ||||||| |||||||||||||||| | ||||||||||||||||| || | || ||||||||||| || | ||| | ||||||| | || ||
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatct--aacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G001223_T03 (Zea mays), 3'ss of exon 1
-------------------aatgggcagtgagatcaatggaattgagtcatgtt-----tcagggcgacaaagtagagtttctgtct-gcag--tcccattctga---gtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| | | | || | | || | || || || | || | || | || |||| | || || | |||| | | | | |||| || | |||||||||||||||| |||| |||||||| ||||| ||| | || ||||||||||| || ||| | | ||||||| |||| ||
gtgaggatccgacgacggagctcgacgatatatccatcgacctcacgttttcttcgcattccattcgttttattatatttgccatccagcagaatataatgctcatctatgcgtgtgcgtctctctgcagGTCTGCGGCGGTGCGGCAAGAGCTGCCGGCTCCGGTGGACCAACTACCTGCGGCCGGACATCAAGCGGGGCAAGTTCACGCTGCAGGAGGAGCAGACCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 1
-aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccat--tctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
|| | || || | || | | ||| || | || | ||| | | |||| | | |||| |||||||| ||| | || |||||||| || ||||| ||||||| |||||||||||||| ||||| ||||| || | || ||| ||||| || | | |
taaaagaatacttgaccatttattctgtttttttttttt---taacttaatattcatgacctctacgtttccatagatttataagattaattttcactttcagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
aatgggcagtgagatcaatggaattgagtcatgtttcaggg--cgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
| || | | | || | | | | | | | |||| || ||| || || | | | || || | ||| | ||| || | || || ||||||||| |||||||||||||||||||||| | || ||||| ||||| || | || ||| || || || ||
gttaggtctctaaag-attgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactt-taacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
upper sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 1
aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
||| | | ||| ||| | | || | || | |||| ||| | ||||||||||| || |||||||| |||||||||||||| | || || || || ||||| | || | | | || || |
-----------------------------------gtgaatcgatttctcacatcttcgtctcatagtttctcttgga----------tcttgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAACTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT---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|18344064|gb|BJ176103.1|BJ176103EST: CATTCAGGAACACGGTCATGGAAGCTGGCGCGCACTCCCTGAGAAAGCTG GGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGA
genomic: CATTCAGGAACACGGTCATGGAAGCTGGCGCGCACTCCCTGAGAAAGCTGgtacgtcgca ... tttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
8 (upstream exon),
33 (downstream exon)
Score:
3CTGAAGAAGGGGCCGTGGACACCTGATGAGGATCAGAAGCTGGTGGCTTACATTCAGGAACACGGTCATGGAAGCTGGCGCGCACTCCCTGAGAAAGCTGgtacgtcgca ... tttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
cgcattttttttcttt CT-rich tract
attttttttctttca TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG