Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
Basic information
species | Physcomitrella patens |
transcript | PP1S152_13V6.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
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----------------------------------------------ttccacat----atgttgtt-tgcattgcacttgtgtgatgctgttc---ttgaagtaattatattatc-aattggattgtat-tgtttctcatcct-----------gtgtatc-atacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtg-gtaactgttttagctaggtaaagtggatgtgcttcttaactttattagtt-ataatatacctg-tgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
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----------------------------------------------------------------agtcatatgccttctatatca---tatatagtttgtatgtcattgttctaggtctgttgaaccactgtactc----actgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgt-gcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
|| | || ||||| | | | || ||| || || ||| | | || | | ||| | | | | || || | ||| |||| || || || ||||||||||| || || || || || ||||| || |||||||| ||||| || |||||||| || || |||||||||||||| ||||||
-----------------------------------------------------------ttcggttatttctctgcgcgctgtgctatttttaccgaataagttgaaccttttcccacctagtgaaaa----ctttgtgatctcacacgt------atgcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC
upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttctt-----aactttattagtt-ataatatacctgt-gcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
| | ||| |||| ||| |||||| || | | || | | | | || || ||||| | | || | ||| |||| || || || ||||||||||| || || || || || ||||| || |||||||| ||||| || |||||||| || || |||||||||||||| ||||||
-----------------------------------------------------------------------ttttggttatttctccatgt----gttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
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-----------------------------------------------------------------------------------------------------gta-tggtttttttcttatgttctcgatgtaaatgacatttctgtgtgttctatta--------cagTGTTGATAGGAACAAATATCAGATCCAAATACCTTTGCCCCCTAAGATTGATCCGAGCGTCACTATGATGACGGTGGAGGAGAAGCCCGATGTAACTTACMapped 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|208399150|gb|DC912407.1|DC912407EST: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGG GGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
genomic: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGGgtatgtcgtc ... acctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
EST:
gi|162256308|gb|FC432318.1|FC432318EST: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGG GGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
genomic: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGGgtatgtcgtc ... acctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
EST:
gi|162257097|gb|FC432557.1|FC432557EST: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGG GGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
genomic: TTGGGTGAGAAGGTGTCTCCAACAGATATAGAGGAGGGTATGCGTGTTGGgtatgtcgtc ... acctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
tcttaac putative branch site (score: 2)
ttcttaactttattag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG