Sequence
atgc intronic sequence ATGC exonic sequencegtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
Basic information
species | Physcomitrella patens |
transcript | PP1S85_160V6.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S85_160V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 2
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
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-------------------------------gtatgtttatgtg----ttttctgtttgtaataacaacaattgtttatatttctatgttatacgactatagtatgtcccttttacccttttgcagGTTGATGACTGGGATACAATGGAAAGATTTTGGCAACAGTGCATTTTCAACTATCTACGGTGCAATCCTGAAGAGCACTACTTCCTTCTTACCGATAGTC
upper sequence: PP1S85_160V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 2
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
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--------------gtgggcgctccagctgtgtactgccgtgtgccgtgtc--cagttgctgctgttttttcacgaccttacttacgattgaatta--ggctgaaa-------tgaactctttcagGTGGAAAATTGGGATTCTATGGAGAGGTTTTGGCAACAGTGCATCTTCAATTACCTCCGGTGCGACCCAGAAGATCATTATTTTCTTCTAACTGAGAGCC
upper sequence: PP1S85_160V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 2
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
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-------------------------------------------gtagtatatacattttc--ttttagtgatgttgtccttc--atttgtgttctaccttc--atatgccttactg--ttttgcagGTTCATGACTGGGATACAATGGAGAGATTTTGGCAGCAATGTATTTTCAATTATCTACGTTGCAATCCCGAAGAGCATTATTTCCTTCTTACAGATAGTC
upper sequence: PP1S85_160V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 2
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtt-taagtggttgtggtcgtaatattttcgca---ctactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
||| || | || | | |||| | || | ||||||| |||| | | || ||| || | | | || ||| | || ||||||||||| |||||||| || ||||| || ||| ||||||| || || || ||||| ||||||||||||||| | | || ||||||||||
------------------------gtgggcgctccagctgtgtactgccgtgtccagttgctggtgtttttttttcgcgaccttacttacgattgatttgg---------gctggagcgaactctttcagGTGGAGAATTGGGATACCATGGAGAGGTTCTGGCAACAGTGCATCTTCAATTACCTCCGGTGCGACCCAGAAGATCATTATTTTCTTCTAACTGAGAGCC
upper sequence: PP1S85_160V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G305332_T02 (Zea mays), 3'ss of exon 2
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
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-------------agtccaaatcctccagg--ttatgagagggcagccccaagtagttaagat--taatagtt--gcagttcta-------cctccacatgccttatcctcttttctgttttgcagGTTTATGACTGGGATACAATGGAGAGATTTTGGCAGCAATGTATTTTCAATTATCTACGTTGCAATCCCGAAGAGCACTATTTCCTTCTTACGGATAGTCMapped 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|100365851|gb|BY967178.1|BY967178EST: AGCAACACTCAAGTGCGTACACTCTTAGTTATCCCATTCGACAAGGCCAG ATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAAC
genomic: AGCAACACTCAAGTGCGTACACTCTTAGTTATCCCATTCGACAAGGCCAGgtacacgtat ... ctttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
ttttaat putative branch site (score: 3)
ccttcgttacttttt putative PPT
tgttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacgtatcaacctccgcattctggggtacttctttcacgtgaagtttaagtggttgtggtcgtaatattttcgcactactgaagggtgttttaatgtccgacagccttcgttactttttgcagATTGAAAATTGGGATACGATGGAGAGATTTTGGCAGCAATGCCTCTTCAACTATCTGCGATGCGATCCAGAAGATCATTATATGTTACTCACTGAGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA