Sequence
atgc intronic sequence ATGC exonic sequencegtaacttccgcactcattttgtgccactgcttctcaaatttatttccgtgtttattgtgtggcgcattcaagccgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S4_12V6.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
gtaacttccgcactcattttgtgccactgcttctcaaattta---tttccgtgtttattgtgtggcgcattcaagc-cgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------
|||| | | | | || | ||||||| || ||| || | | | | || | | ||| | || | | | || | | | | | || || | | | ||| || ||| ||| |||||||||||||| | |||||||| | || || | |||||||||||||||||| ||||||||||||||
gtaagtggaactttt-tcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagc--aatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
upper sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 15
gtaacttccgcactcattttgtgccactgcttctcaaatttatttccgtgtttattgtgtggcgcattcaagccgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------
| ||||| ||| ||| | | | | | ||| || || | |||| | | || || | | | ||||| || ||| || |||| | | || | | |||| | || ||| ||| |||||||||| | |||||||| | || || | |||||||||||||||||| |||||||| |||||
-----------------------------gtaagtgaattt-tttaaatgtaatataattagtacctccaaaaaaatatgctcgtactc-ctgtgtatatatatca---acttaagcaatcgcaaacttg-----aactttttagtaccac-----gtctaagttgtctctttg--tcagGTTGGTCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCTGTTGATGGCTCTGTGTCCAAGCACCAGGGC
upper sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 14
gtaacttccgcactcattttgtgccactgcttctcaaatttatttccgtgtttattgtgtggcgcattcaagccgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------
| || || | ||| | | || ||| | | || ||| || || ||| | | | |||| || ||||||| || | | ||||||| |||||||||||||| || |||||||||||
-------------------------------------------------------------------------------------------------------------------gtaagcctcagttttttccccaggggtggg-tcttccctgacagtg-----tgagcatg---cagAATAGTGTCAGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGA
upper sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 14
gtaacttccgcactcattttgtgccactgcttctcaaatttatttccgtgtttattgtgtggcgcattcaagccgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------
| || | ||| | | | || || | ||||||| | ||| | | || |||| || ||||||| || | | ||||||| |||||||||||||| || |||||||||||
-----------------------------------------------------------------------------------------------------------------gtaagcctcaggttttttccccaggggtgggtcttccctgacagtgtgagc----------atgcagAATAGTGTCGGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGAMapped 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|37851638|gb|BJ609646.1|BJ609646EST: CTCATGGCTCATCTTGTTGATCTCCAATCAAAGCTTGGCGATGTGAACAA AGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATG
genomic: CTCATGGCTCATCTTGTTGATCTCCAATCAAAGCTTGGCGATGTGAACAAgtaacttccg ... ctctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA
tattaat putative branch site (score: 2)
ctctgctc putative PPT
ttattaatgcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttccgcactcattttgtgccactgcttctcaaatttatttccgtgtttattgtgtggcgcattcaagccgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA