Sequence
atgc intronic sequence ATGC exonic sequenceAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
Basic information
species | Physcomitrella patens |
transcript | PP1S99_260V6.1 |
intron # | 21 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 21
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttt-taatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
|| || ||||| |||||||| || || |||||||| |||||||||||||| |||||||| || || || ||||| ||||||||||| ||||| || ||||| || || | || | || | | | | | | | | ||| || | || | |||| || | || ||| | | | |||||
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgat---attct--cttaatggttctcacc---gcaagtgattaaactagt--caaataatgtttctcatttcctcttaccagatgaat-----cagatcttgtgagatt----------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgc-ttttgtgatttgtcacacttgtgttgatgcatatgtctcg-gttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
|||| | || ||| | |||||||| || |||||||| |||||||| || || |||||||||||||| || || || || || ||||| | || ||||||||| || || | || |||| | | ||| |||| | | || | || ||| | | | | | |||| | | |
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata----------cataaaatttgcacatactgtaatttattgagccattgct-attcatttatattgagctttattttctttccag--------------------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 23
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttga-tgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||||| |||||||||||||||||||| ||||| ||||| || ||||| || |||||||| || || || || || || |||||||| || | |||||||||| | || | | ||| || | | ||| || | ||| | | | | | | || || |
GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtat-tcatggtggctttgtt------------tttctttcattgcacagatagaagttaagtatgacttatttgctctttgtacag--------------------------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 8
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||||| ||||||||||||||||| || ||||| ||||| || ||||| || |||||||| || || || || || || |||||||| || | |||||||||| | | | | ||| || | | | |||| || | || ||| | | | || || |
GGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtat-tcacagtggctttgttt------ttctttccattgaacaggacacagttagtatatggcttatttat---tctttgtacag--------------------------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA13G44420.1 (Glycine max), 5'ss of exon 22
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgt-cacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||||| ||||||||||| |||||||| || || |||||||| |||||||| || ||||| ||||| | ||||| || |||||||| ||||| |||||||||| || || | || ||| | || | ||||| | ||||| |||||| | | | | || |
TGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCATTCAAATATATAATGTCCGTGTAGATGAGgtat--cattgctgcccataaacatttcctgctcagtttttatttgagtaataaggtgtttatgcattttttttcttctttgcag----------------------------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA13G22720.1 (Glycine max), 5'ss of exon 22
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| || || | || || || ||||||||| | ||||| ||||||| ||| || ||| || || | | || | || || || || || || | | | ||| | || || | ||| | || | || |
AGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtat--tat----tctatgcacaatgccttaagatatta-gtttagtttca--tgcatt-ataggtgttttaaaaatttgacattgagcttttgttta---atttgttttaatctag-------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA17G12110.2 (Glycine max), 5'ss of exon 22
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtat----------gttatcaagtcc----ttgccagataagttgcgctt--ttgtgatttgtcaca-cttgtgttgatgcatatgtctcggt-tttaatataagactgtcgttgatacgcttaat--aagatttctctgctgttcacag-------------------------------------------
||| || || ||||||||||||||||| |||||||| ||||| |||||||| || ||||| || || | || || || ||||||||| | ||||| ||||||| ||| || | || | |||||| | | |||||| | | | | || | | |||| || | | || | | || | ||| | | | || || |||| |
AGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactctatgcacaatctagactagagctgttggttaagtttcataaaataatgattttttaaaattcgtacaagtctctccctctcctccttccacacaatgccttaagacattagtttagtttcatacgtcattggtgttttaaaaattttgacattgaccttttttgtttaatttgttttcatctag
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA19G41840.3 (Glycine max), 5'ss of exon 21
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcg-gttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
|| |||| ||||| || || || || ||||| ||||| ||||| || || || ||||| ||||| |||||||| || ||||||||| | ||||||||||| ||| | || || | | | || |||| ||||| | | | | || || |||||| |||| | | | | | |
TGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAATTCACATATATAATGTTAGAGTGGATGAGgtg-attacta--tctttaactgttt--ttttcattttaagatttatgttattatttttaatt----tgtctcatattttctcttgggtgtatattctag-------------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 5'ss of exon 21
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||||| || |||||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| || || || ||||||||| || ||| ||| || | |||| || || || | |||| | | | || | || ||| | | || ||||| |
TGCAGCAACATTTCTTGCTTTCCATCCTCAAGATAACAATATTATTGCTATCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagta------------cagttaa--tgggtagttgtcatacatccca--tatgttaacaagcaagacttcttatttggataccattttc-ttgatgcag---------------------------
upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 21
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
||||| |||||| | || || ||||| ||||| || ||||||||||| || |||||||| ||||| |||||||| || ||||||||| | || |||||||| || || ||| ||| || | |||| ||| | || | ||| | || || | |||| | ||| |||| |
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt--gtttttgttgattaattt---ttcctgtgtttttaattgttaaagtcaaattctatcttcaagt---ggaatgatgatgtcttgcatatgcttttt----------------------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|162243462|gb|FC425158.1|FC425158EST: ATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAG GTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTC
genomic: ATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatc ... ctgttcacagGTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTC
EST:
gi|162177514|gb|FC353775.1|FC353775EST: TCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAG GTGAAAAGCAAGTTGAAGGGTCATCAA
genomic: TCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatc ... ctgttcacagGTGAAAAGCAAGTTGAAGGGTCATCAA
EST:
gi|162279738|gb|FC455646.1|FC455646EST: TCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAG GTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTC
genomic: TCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatc ... ctgttcacagGTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTC
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:
33 (upstream exon),
35 (downstream exon)
Score:
5AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatc ... ctgttcacagGTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTCTCTAACACTCTCAATGTTCTTGTATCATCCGGAGCGGATGCTCAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA