Sequence
atgc intronic sequence ATGC exonic sequence...gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC
Basic information
species | Physcomitrella patens |
transcript | PP1S399_19V6.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtg-ttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC------------
| | |||| | | | | ||| |||| ||| | | | || | | || || | | | | | | | |||| ||| | |||||| | |||||||| ||||||||||||||||||||||||||||||||||| || ||||| | |||||||| |||| |
-------gatatgtgtaatcttgtta---gctaaatcataattttcg-tatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtt--tctatagaaagATGGCGTCTCACATTGTTGGATACCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCCTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCTGAGGATT
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgc-gttgg-tgcatctcg--ttcggtatcgaaccgaggtatatcttcgttggctaatgtg-ttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
|||| || | | || | || ||| | | ||| || |||| | | | || | | || || | | | | | | | |||| ||| | |||||| | |||||||| ||||||||||||||||||||||||||||||||||| || ||||| | |||||||| |||| |
----gttagcatatggatatgtgtaatcttgttagctaaatcataattttcgtatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtt--tctatagAAAGATGGCGTCTCACATTGTTGGATACCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCCTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCTGAG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.2 (Oryza sativa), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtg-ttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
| | | |||| | | | | ||| |||| ||| | | | || | | || || | | | | | | | |||| ||| | |||||| | |||||||| ||||||||||||||||||||||||||||||||||| || ||||| | |||||||| |||| |
---tatggatatgtgtaatcttgtta---gctaaatcataattttcg-tatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtt--tctatagAAAGATGGCGTCTCACATTGTTGGATACCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCCTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCTGAG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatc-gaaccgaggtatatcttcgttggc-taatgtgttgcacctc--tctcacagATTTCA-AGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
| | | | || ||| || | || | || | ||| | | || | |||| | | | | | || | | || || |||| ||| | || ||| | |||||||| || |||||||||||||||||||||||||||||||| |||||||| | |||||||| |||| |
---------agcatg-accttaatcata---tcgttctcatcaataaacatctgtattccttgttacaatagttgacatggtatttctgactgtaattctatttatggcacagAAAGATGGCGTCCCACATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCACTTGAGTCTTTCTGGGATGGGAAGAGCACCGCTGAG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G149751_T03 (Zea mays), 3'ss of exon 1
-gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC------------
| || | || || | || || || | | | ||| | | | | | | || | | |||||| |||| || | || ||| | |||||||| || |||||||||||||||||||||||||||||||| |||||||| | |||||||| |||| |
tgaccttaatcatatcgttctcatcaataaacatctgtattccttgttacaatagttgacatggtatttctgactgtaattctatt-----tatggcacaga----aagA----TGGCGTCCCACATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCACTTGAGTCTTTCTGGGATGGGAAGAGCACCGCTGAGGATC
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G112149_T02 (Zea mays), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC------------
| | || | | | | | |||| ||| | | | || | | ||| | || || || | | | || | | | |||| ||| | || || | |||||||| || |||||||||||||||||||||||||||||||| | ||||| | |||||||| |||| |
------tcttttagcttatttgcagctttgttgaggcaaatattcagctagcttctc------tatttctgtgaatcaacctgatcttaagattttactgttatatagaaagATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAGGATT
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G112149_T01 (Zea mays), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
| | | || | | | | | |||| ||| | | | || | | ||| | || || || | | | || | | | |||| ||| | || || | |||||||| || |||||||||||||||||||||||||||||||| | ||||| | |||||||| |||| |
--gagctcttttagcttatttgcagctttgttgaggcaaatattcagctagcttctc------tatttctgtgaatcaacctgatcttaagattttactgttatatagAAAGATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggta-tatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
| | || | | | | || ||| | | | || || | || || ||| || | | | || | ||| | || |||| ||| | || || | |||||||| || ||||||||||||||||| |||||||||||||| | ||||| | |||||||| |||| |
--gctagagagagctcttttagcttat---ttgcagtttttttttgggacaaatattcagctagcttctctgtcaacctgattttaacatttttctgttatat----agAAAGATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGAGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAT
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G29180.2 (Glycine max), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcgg--tatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC--------
|| || | | | | ||| | | | | |||| ||| | || | | |||||| || | ||| |||| ||| | |||||| | |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||||| | ||||||||||||| |
------tattgc-catgatctatggattttgttgcatgtgttattcgttttatttatggagagtggacaagtgagagctaatttggagttttgatctgttgcgac---agAAAAATGGCATCTCACATCGTTGGATACCCCCGCATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCGAG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC------
||| ||| | | || | || | | | | | | | ||| || | || || || || ||| || || ||| | |||||| | |||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| | ||||||||||||| |
---gttgcatgtgttaatgcggatattattgccatgatctatgaattttgttgcat-gtgttat-tcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAA-ATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
upper sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0056g01570.t01 (Vitis vinifera), 3'ss of exon 1
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC-----
| || | | | || | || | | || | | || | || | | |||| | ||||||| | | | | | | || || ||| | || ||| | ||||||||||| |||||||| |||||||| |||||||| |||||| | || || | |||||| |||| |
-tatttgaatttttgttgtttgatttgatggtaacttattt-gaaaagttgcaaagaaattgaaatctgaatgaaggaatgtgtgacgaatttgtgatgaaaC---AGCACAATGGCGTCCCACATTGTTGGATATCCTCGCATGGGGCCCAAGAGAGAGCTCAAATTTGCTTTGGAATCATTTTGGGATAAAAAGAGCAGCGCCMapped 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|67718678|gb|BJ968937.1|BJ968937EST: AGCAGAGTGTGGCTCGGTTCAGATCTGAGACTTTTGTATCGAGTTGTGTC ATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCC
genomic: AGCAGAGTGTGGCTCGGTTCAGATCTGAGACTTTTGTATCGAGTTGTGTCgtgagtcttc ... tctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC
ggctaat putative branch site (score: 3)
cacctctctc putative PPT
tatatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA