Sequence
atgc intronic sequence ATGC exonic sequence...ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
Basic information
species | Physcomitrella patens |
transcript | PP1S220_83V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 1
----ggacgtgccacaaaattgattgtca-acagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
||| | ||||| |||||| | || ||| | | | ||| | | | | | | | | | ||| | | ||| | ||| ||||| ||||||||||| ||||| ||| | | || |||||||||||| |||||| ||||| ||||||||||| ||||||||||| ||||||||| |||||
gtgtggaaacattattaaatt-attgtcggatagtgaattggaattgctagctgctttcatacaaaaccggccacttatctta---tgcttttgtgttctg-cagGCGTTGGACAAGATCAGGTTCGAGAGCTTGACGGACAAGAGCAAGCTGGATGCTCAGCCAGAGCTGTTCATCCATATTGTTCCTGACAAGGCCTCCAACA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os09g30412.1 (Oryza sativa), 3'ss of exon 1
ggacgtgcca-caaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactgga-gttggttctcatttgttactt-tacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
|||| | | || | || | | | | | ||| || ||| | || | || || | | | || ||| ||||| ||||| ||||||||||| ||| ||| || |||||||||||| | |||| |||||| ||||||||||| || ||||| ||||||||||| | |||||
--gcgtgtaatctgtatagtgtggtagtgtgctgatgcttttacagatctgtgtgtttgggtgatgaattcgatgtgacatgggtgtgtgtggtttctg-cagGCATTGGATAAGATTAGGTTCGAGAGCCTCACGGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTCCCCGACAAGGCTAGCAACA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G012631_T01 (Zea mays), 3'ss of exon 1
ggacgtgccacaaaattgattgtcaacagcgaaacagt----aatttatgcttgtatgactggagttggttctca--tttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
| ||||||| ||| | | | | | ||| ||| || | | | | | ||| | | | || || ||||||||||||||||| ||||||||| | || ||||||| |||| |||||| ||||| ||||||||||| || ||||| |||||||||||||||||||
------gtgacaaaatacatttgaagtccctgtgctcttctgggatgatggttgaatcaaactactaagccactaaccttgatgtctctctgctgtttccaaacagGCCTTGGACAAGATCAGGTTTGAGAGTTTGACGGACAAGACCAAGCTGGATGCACAGCCAGAGCTGTTCATCCACATTGTCCCCGACAAGGCCAACAACA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------------------ggacgtgccacaaaattgattgtcaaca-gcgaaacagtaatttatgcttgtatgactggagttggttctcatt-----tgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
|| || | | ||| | | | | || | | || || | || || || | ||| | || | ||| | || ||| ||||| |||||||| || ||||| ||| ||| || |||||||||||| | |||| |||||| ||||||||||| || ||||| || |||||||| ||||
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctg-cagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA---------------------------------------------------------
| | | | | || | | | ||| | || ||| ||||| |||||||| || ||||| ||| ||| || |||||||||||| | |||| |||||| ||||||||||| || ||||| || |||||||| ||||
-------------------------------------------------------tttgcgctcctacttggt-gctgttttttgtgcgacttctg-caggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
---------ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
| |||| | | || | | | | | | | | | | ||||||| | | | |||| ||||| ||| || ||||||||||| ||||| ||||| ||| | || |||||||||||| |||||| ||||| ||||||||||| || || || || |||||||||||||| |
tcatcccttgtttgtgctatactcttattactgcatggttaggctgcacta---ggttgtatgcatcaaaccaacg---aactgtttcttta---ttgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA18G08220.1 (Glycine max), 3'ss of exon 1
ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtat-gactggagttgg--ttctcatttgttactttac-gcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
| || || || | | | | ||| | ||||| | || | | || | | ||| ||| | | | || | | |||| |||||||||||||| |||||| | || |||||||||||| | |||| ||||| ||| |||||||||||||| ||||||||||| | |||||
--tttttttactgtgatgtgtggttgtggtaatattg-gttttcttcttgtgttgatttgtcctgacatattaattaattatgtggctgtatgtaaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGATGCTCAGCCAGAGTTGTTCATTCATATTATTCCCGACAAGACTAACAAT-
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA14G01530.1 (Glycine max), 3'ss of exon 1
ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggtt-ctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
|| | | || || | | | || | ||| ||| | | | || || || | | | |||| || | | |||| |||||||||||| | |||||| || || |||||||||||| | |||| ||||| ||| |||||||||| ||| |||| |||||| |||||||||
atttgttctgaattatgctttattta-ggttttctcttattctattctttgggcattatatctgattgctgacatatgttattacctttacaacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGATGCTCAGCCAGAGTTGTTCATTCACATTATTCCTGACAAGACCAACAACA
upper sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G47210.1 (Glycine max), 3'ss of exon 1
---ggacgtgccacaaaattga---ttgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
|| || || | || || | | | || | | || || ||| | | | |||| | ||| |||| || | | |||| |||||||||||| | |||||| || || |||||||||||| | |||| ||||| ||| |||||||||| ||| |||| |||||| |||||||||
tttcgat-tggcattgagttatgcttttttagttttttccctctactctttgggcaaatatctga---ttgctgtcatatttta--ttacctttactacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGATGCTCAGCCAGAGTTGTTCATTCACATTATTCCTGACAAGACCAACAACAMapped 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|100439764|gb|BY962096.1|BY962096EST: ACAGTAACAAGGAGATATTCTTGAGAGAACTCATCAGCAACTCTTCTGAT GCCTTGGACAAGATTATGTTTGAGTCCCTAACCGACAAGAGCAAGATGGAT
genomic: ACAGTAACAAGGAGATATTCTTGAGAGAACTCATCAGCAACTCTTCTGATgtaggtgttt ... gccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
atttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT