Sequence
atgc intronic sequence ATGC exonic sequencegtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
Basic information
species | Physcomitrella patens |
transcript | PP1S1_78V6.1 |
intron # | 2 |
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 2
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttt-tttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
||| || | | || | || | |||| | || | || | | ||| | | ||| | | | | || | ||||| |||||||| || || | || || || | | |||||||||||||| || |||||||||||||| ||| |||||||| |||| | || | ||| ||
-----------------------------------------------------------------------------------tgatactgactgctgctagctagata-gctagctcaatcctgctagctgtttgatattctaatttctaagtaagctgttgctgtcatgatcaaacctgcagGTGGTCAGCCATTGCCAAGCACCTCCCAGGTAGGACTGACAACGAGATCAAGAACTACTGGAACACACACCTGAAGAAGGATCTGATCCAGAAGGGCATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| ||||| | | | || ||||| || | || || | | | || || | | ||| || | | | |||| || |||||||| ||||| || || || | || || || ||||| ||||||||||| || |||||||||||||| ||| | |||||||| ||| | ||||||||
-------------------------------------------------------------------------gctgtttgtttaattttgtcactgcgaa------tggagggcttttgacgtgcgattttcctgatcttttttcttggccggcg----ttggcgttgttgttgttttgcagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTAAAGAAGCGGCTGGCCAAGATGGGGATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
|| | | || | | | | | ||| |||||||| | | | || | | || | | | ||| ||||| || || || | || || || || || ||||||||||| || |||||||||||||| ||| |||||||| | || ||||| ||
--------------------------------------------------------------------------------ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaat--aaaaggtaactgacactcagacgcacgtac-acagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcg-aagttccatgtggta--gccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
|| | || | |||| | || | || | ||| | || | | || | || ||| | | | | | |||| ||||| | || || | || || || ||||| ||||||||||| || |||||||||||||| ||| | |||||||| || | ||||| ||
--------------------------------------------------------------------------------ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgact--gacaatgacat--gccctcgcgcaaccc--gcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G032655_T01 (Zea mays), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttat-tgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| | | ||| || | | || || || || | ||| | ||| || | | | || | | ||| | ||||| ||||| || || || | || || || ||||| ||||||||||| || |||||||||||||| ||| | |||||||| ||| | ||||| ||
--------------------------------------------------------------------------------ttacgctgctgccgttgtagattt----gtcaacgcgatcgctgataattgttttcccctcatgggctcatggcgcgcgtccgccgtgcgtgcaatgcatgcagGTGGTCGGCGATCGCGACGCACCTCCCGAAACGCACCGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTGGCCAAGATGGGCATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| ||| | | | | || | | | ||| | || ||| | | | | | ||| || | |||| || | ||| ||| | || ||||| ||| | || | | || ||||| |||||||| |||| |||||||| ||||||||||||||||| |||||| ||
-------------------------------------------------------------------------------tacataaaattgctggtttg---tttctttgaattacctgaatcagttcaaattcatattttaaatgcacatttatgactatatacattgaacaaattct-cagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| ||||| | | || |||| | | | | | | | | || || | |||||| | || || | || || ||| ||| | |||||||| ||| || || | | || ||||| ||||||||||||| |||||||| ||||||||||| ||||| | ||||| ||
----------------------------------------------------------------------------catgtcatgtagagattagtagaaa---ccatataatgatttctctctttttctttaaggctata-tattttga-cagtg-ttcaaaaaaatgaaccaattc-acagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G39720.1 (Glycine max), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacg-atggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
|||| ||| ||| || | || | ||| || | || | | || | |||| || | || | || || | || ||| ||| | || ||||| ||| | || | | || ||||| |||||||| |||| ||||| |||||||||||||||||||| |||||| ||
---------------------------------------------------------------------------tgttaacatagt-------acgtaaaaatttctggtttgttctttacctgaatcagttcagattct-tattttaaaggcatatttatgactag-ataaacaaatttcagGTGGGCTGCAATAGCCTCTCAATTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAATACTCACTTGAAGAAGCGTCTCAAAAGAATGGGTCTT
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
|||| | |||| || | || | || || || | | || | ||| | ||| | | || | | || || | || | || | | | | | | | || | | | || || || | || | || ||||| || || || || | | ||| | | || ||||||||||| |||||||| |||||||||||| | | || | || || | ||||| ||
gtgag--tttgaacttttcaataattttatatttttg------ccattacgtagtttatacgaaaac--tactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgct------ttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ18565 (Selaginella moellendorffii), 3'ss of exon 1
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttat-tgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| |||||| | ||| | ||| || | || | | | |||||| || ||| ||||| | || || || ||||| | || ||||||||| |||| ||||||||||||||||| ||| | ||||||| || |||||||||| ||
------------------------------------------------------------------------------------------------------------------gtaacagtttgtagagttttacctctaaattcttg--cgttctctaagctcttgcgtgtttcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACAAGATTAAAAACTACTGGAACACACACCTCAAGAAGCAATTGTTGCAAATGGGAATC
upper sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 2
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctg-gttattgtgtttttt--ttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
| ||| | | || | |||| ||| ||| |||| | || ||| ||||| | || || || ||||| | || |||||||||||||| |||||| |||||||||| ||| | ||||||| || | || |||||||||
---------------------------------------------------------------------------------------------------------------------------------------gtaagagtttgtagagttttacctctaagttcttgcgtttctcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAGCAATTGTTACAGATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
tgtttttttt CT-rich tract
ttattgtgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC