Sequence
atgc intronic sequence ATGC exonic sequencegtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
Basic information
species | Physcomitrella patens |
transcript | PP1S1_78V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 1
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaa-attcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| ||| || | | | | ||||| | | | ||| || | | | | | | | | | | ||| | | | || | |||| || | | || || |||||||| || ||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||| || ||
------------------gtgagcgcgcgcgtcagctttgctctgccgccattgatgagcatgcacaaagctagcttagattagcttatcttatgaatggtaactgatatatccagcttctttgtttgtgcagGGCTCTCGAGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGTGGTCGCTTCTCCTTCGAGGAGGAGGAGGCCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g37970.1 (Oryza sativa), 3'ss of exon 1
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttt-tatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| || | | || ||| |||| |||| | || ||| | |||| || |||| ||| | | | || | ||||||| |||| | | | |||||||||||||| | ||||||||||||||||||| ||||||||||||||| | || ||||| || |||||||| |||| ||
-----------------------tcgaaaagcactcattt-gcacaatg-attg-tagaatttaacacctgatatctgaat-------cttctgctgatctagcctgatcaatgaacaccttgtgattcgcagGTTTGAACAGGTGTGGCAAGAGCTGCAGGCTGCGGTGGACGAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCTCCCAGGAGGAGGAGCAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| | || | |||| | | | | | | | ||| | | | | || | | | ||| ||| | | | | ||| || || |||| || | || || ||||||||||| || ||||||||||||||||||| |||||||||||||||| || | ||| | |||||| | || ||
--------------------------ctctcttttcgtgcatgagaa-gtactcggtattattcacagg---agctgagagactctagtccgttccatctggataacact--tcgttttgcgttgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 1
----gtacatat---tcatttgcaaccggataagcga-gtagtgatg---gagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|||| | || ||||| | || | | | | | | | || | || | || | | | |||| | ||| |||| | | | | | | || | | |||| || | || || ||||||||||| || ||||||||||||||||||| |||||||||||||||| || | ||| | | |||||| || || ||
gtacgtacgttcgtctcttttgcgatcgatctggggccgccgcgtcgcgcgcgcgtggtccagtagtgcttccgtttcgttttttttgtgcggttttcgctgaggcgaggcgcgtgtgcgcgatcgatgggtgcg---tgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTGCGGCCGGACATCAAGCGCGGGCCTTTCACCCCGGAGGAGCACAAGTCCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 1
-------gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacattt--ttatcgaaacggctttctttcttt-ctttctttctttctttatttatttcttgtgaa----attcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| ||| | | || | | | |||| || | || | | | |||| | | | || ||| || | | | || | | || || | |||| || ||||| || ||||||||||| ||| | ||||||||||||||||| |||||||||||||| | || ||| | ||||||| |||| ||
gtaagcgccgcttatctagcttaaatttcttc--tcaacctctgcaatcctagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 1
gtacatattcatt-tgcaaccg-gataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|||| | ||| | | | | || |||| | | | || | | | | | || ||| || | ||| || | | || | |||||||| || | ||| || ||||||||||| || | |||||||||||||||||| |||||||||||||| | || ||| | | ||||||| |||| ||
gtacgtgcgtgccatgcgatctcggttttcggcctctgat--aactagctaaatcgcctgatcgatccgcc--------aattgctcactggtgtggttttttgggggaatgcgtgtgttgacgcataattcagGGCTGCGGCGGTGCGGCAAGAGCTGCCGGCTCCGGTGGACGAACTACCTTCGGCCGGACATCAAGAGGGGCAAGTTCACGCTGCAGGAGGAGCAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------gtacatattcattt--gcaaccggataagcgagtag-tgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttattt--atttcttgtgaaatt-cagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|| || | | | | | | || || | | | | || | | || || ||| ||| || | | | | ||| | | ||| | | | || |||| || | || || ||||||||||| ||| ||||||||||||||||||| |||||||||||||||| || | ||| || |||||| | || ||
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtg-atgcttctcgct-cggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G111045_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtacatattcatttgcaaccggataagcg-agtagtgatggagcagaa----tgcattggttcgtttctacatttttatcgaaacggctttctttctt---tctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| ||| | || | ||| ||| || || || ||| | | | ||| | | | ||| || | | | ||| || | ||| | | || || |||| || | || || ||||||||||| ||| |||||||||| |||||||| |||||||||||||||| || | ||| || |||||||| || ||
gtcagaattcctctctttattagtcccttctcttcgcggtttccaccgtcgtcgtcttagcttagttctgcccgaccattggtgtcgcactcgcactggcctaaaatgccgaccaaattcctcgccggagtgaacgatgcttactctatttctgggatggcaatggcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACCAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACAGCCGAGGAGGAGAAGTCCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G166337_T01 (Zea mays), 3'ss of exon 2
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|||| |||| ||| ||| | || || | | | | | | | | || | | | | | || ||| | ||| || || || || |||||||| || |||||||||| |||||||| ||||||||||||||||| || || ||||| |||||||| || ||
---------------------------------gtgagcgagcgacctgc--tggccccgatcgacgtcgatcatgcgcatatatacacatatccatgctcacctcgatcgtccttctcatgtcatggcagGGCTCGCA-CGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACTAACTACCTGAGGCCGGACATCAAGCGCGGCCGCTTCTCCTTCGAGGAGGAGGAGGCTAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G032655_T01 (Zea mays), 3'ss of exon 1
gtacatattcatttgcaaccggata-agcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaatt-cagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|| | | | || | | | || | |||| | | | | | ||| | | | || | || | ||| | | || | | |||| | |||| || ||||| || ||||||||||| || | ||||||||||||||||| |||||||||||||||| || ||| | ||||||| |||| ||
gtgagcttgctatagcgagctagtgtagttactagttagtaacaatcaaagtccagcagcattcggctacgctgtttggtttgcgctggctcctccttgacatgcatgcggatatggc-cgtgtggtgtggcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGCCTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G110135_T01 (Zea mays), 3'ss of exon 1
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttat-cgaaacggctttctt-tctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
| || | | || | | | | || | | | | || | ||| | | | ||| || || | | | || | | || |||| || | | || ||||||||||| || |||||||||| |||||||| |||||||||||||||| || ||||| | |||||||| |||| ||
------------gtacatgcatgcatgcatgcccttctccgtccgatcgtctgtctgtctagctgtagctttgtatggattagctagctgatcagcgatggaggagctagctgaacatatatatatgcatgcagGGCTGAACAGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACCAACTACCTGCGGCCGGACATCAAGCGGGGCAAGTTCTCGCGGGAGGAGGAGCAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G111117_T01 (Zea mays), 3'ss of exon 1
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|| || | ||| | | | |||| | | || | | | | ||||| | ||| | ||||| |||||||| | ||| ||||||| |||||||| ||||||||||||||| | || ||| | || || |||| ||
------------------------------------------------------gtgagtatggacagacctgaattctctaccatcttccaaatgaacgaagcttgtgagatctcgagcaacatactgcagGCTTGCAGAGGTGTGGGAAGAGCTGCAGGTTGAGGTGGACAAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCAGCTTGCAAGAAGAACAGACCAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G123202_T01 (Zea mays), 3'ss of exon 2
--------gtacatattcatttgc---aaccggataagcgagtagtga-tggagcagaatgcattggttcgtt-tctacatttttatcgaaacggctttctttctttctttctt----tctttctttatttatttcttgtgaa---attcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|||| | || || | | | ||| | | ||| || | |||| | | ||| | | | | ||| | ||| | | | | | || | | | | | || |||| || | || || ||||||||||| || |||||||||| |||||||| | |||||||||||||| || | ||| | | |||||| || | ||
gtacgtacgtacgtgctctgttcctcggtcgagcccagcccgggccgcctggtgctgcatgcgtgacctagttgttcgcctcgtgctcgtcatttcttgagcgactcgtggtgtaaaatgcgatgtgatgtgccgcgcgcgcatgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACCAACTACCTGCGCCCGGACATCAAGCGCGGGCACTTCACCCCCGAGGAGCACAACTCTAT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G001223_T03 (Zea mays), 3'ss of exon 1
gtacatattcatttgcaaccggataagcga-gtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
|| || | | | | ||| || || || | | | | || | |||||| | || || | | | | || | ||| | | | |||| || | ||| || ||||||||||| || | |||||||| |||||||| |||||||||||||||| || ||| | | ||||||| |||| ||
gtgaggatccgacgacgg--agctcgacgatatatccatcgacctcacgttttcttcgcattccattcgttttattatatttgccatccagcagaatataatgctca-tctatgcgtgtgcgtctctctgcagGTCTGCGGCGGTGCGGCAAGAGCTGCCGGCTCCGGTGGACCAACTACCTGCGGCCGGACATCAAGCGGGGCAAGTTCACGCTGCAGGAGGAGCAGACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
ttctttctttctttct CT-rich tract
tttctttctttctttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttatttatttcttgtgaaattcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG