Sequence
atgc intronic sequence ATGC exonic sequence...agtaatattagctggggtggccatgtttctctgttttttgtataatctgttttcatgcaaacaaacaatgactagtacatcgcgtgattttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
Basic information
species | Physcomitrella patens |
transcript | PP1S83_28V6.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g53790.2 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------agtaatattagctggggtggccatgtttctctgtttt-----ttgtataatctgttttcatgcaaacaaacaatgactagtacatcgcgtgattttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
| || | || || | ||| | || || |||| | | | | || | | | | | | || | || | | ||||||| ||||| ||||| |||||||||||||||||||| |||||||| ||||||||| | || || ||||| || ||| | ||| | || || |||||
gtaactgcttaccttctactttatgtttgattataatgtaagtctcatatgagaggaaacgaacttataggaaactttagatatgcaatgaattgacatgataaaatttaagtacttacatagttatatattatatataaataaagagatatattatcttctgtttctaaccaaaaatttacacagGTGGTCCTGGGAGTGGAAAGGGCACACAGTGTGCCAACATTGTTGAACACTTTGGATTCATTCATCTTAGTGCTGGAGACCTTTTGCGTGCAGAGATCAA
upper sequence: PP1S83_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g43170.1 (Oryza sativa), 3'ss of exon 3
agtaatattagctggggtggccatgtttctctgttttttg--tataatctgttttcatgcaaacaaacaatgactagtacatcgcg--tgatt-----ttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
|||| | || | | || | | |||| | ||| || | ||| | || | | | || | | | ||| || | | |||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||||||| ||| ||||||| || ||| | ||| | || || || ||
-gtaa-accgtcttcgttcctcagttatgtctgactattgatcatccttaaacatcacaaatacttagggtaaataaacttttgtgtctgaccaagaatttgcacatagGTGGTCCTGGAAGTGGAAAAGGCACACAGTGTGCCAACATTGTGGAACACTTTGGATTCACCCACTTAAGTGCTGGAGACCTTTTGCGTGCAGAGATAAA
upper sequence: PP1S83_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g02000.1 (Oryza sativa), 3'ss of exon 3
---------------------------agtaatattagctggg--gtggccatgtttct-ctgttttttgtataatctgttttcatgcaaacaaacaatg-actagtacatcgcgtgat--tttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
| | | | ||| || | || | || | | || | ||| | | | | | | | || || ||| ||||||||| ||||||||||| || ||||| || |||||||| |||||| | ||||| ||| ||| || ||||| || || | | | | ||| ||
gtatgcctatctgtttttaaactaacccactgtgctgaataagtagtgctcacactactacaagcttcagcttttcctagtactatgtgacttcatactccattgagcttttgctgaatcatttaatttgcagGTGGCCCTGGCAGTGGCAAAGGCACTCAATGTGCCAAAATTGTTAAGCAGTTTGGCTTTACACATCTGAGTGCTGGTGATCTCCTTCGTGAAGAAGCAAA
upper sequence: PP1S83_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM5G801436_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------agtaatattagctggggtggccatgtttctctgttttttg---------tataatctgttttcatgcaaacaaacaatgactagtacatcgcgtgattttgga---atgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
|| | | |||| | ||| | | ||||| ||| | |||| | | || | || | |||| | | | ||||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||||||| || || ||||| || || | ||| | || || || ||
gtatatgttctatcttcagtaattttcagttatttgtgtcctaacatagaagagatttttgggttatttgtgtcctaccataaaagagaaggagcttataacaactttgaactcaaatagatgat--tttgttttgcatctgatcaagaatttacacagGTGGTCCTGGAAGTGGAAAAGGCACACAGTGTGCCAACATTGTGGAACACTTTGGATTCACCCATCTTAGTGCTGGAGATCTTTTGCGTGCAGAGATTAA
upper sequence: PP1S83_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv16s0022g00980.t01 (Vitis vinifera), 3'ss of exon 3
-agtaatattagctggggtggccatgtttctctgttttttgtataatc-tgttttcatgcaaacaaacaatgactagtacatcgcgtgattttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
| | | | || | | ||| || | || |||| |||| | | || | ||| | || ||||||| ||||| ||||| || || ||||| ||||| ||||||||||| |||||||||||| |||| ||||||| || || |||| || |||||
tactgaaaagccctctaattatttctggcgaccgttgttcacactataacattttgttgcatgttcatgaaatttaattcattttgctccattct--ctcagGTGGCCCTGGTAGTGGAAAAGGTACACAATGTGCAAAGATTGTTGAGACCTTTGGATTTACACACATAAGTGCTGGAGAACTGTTAAGGAGGGAAATATCMapped 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|162221997|gb|FC398564.1|FC398564EST: GGCCGCAAAGCGCAGTCCTGTCAAAGACTTGAAAGTTGTCTTTGTCTTGG GTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCT
genomic: GGCCGCAAAGCGCAGTCCTGTCAAAGACTTGAAAGTTGTCTTTGTCTTGGgtatgtgtgg ... tggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCT
EST:
gi|18373209|gb|BJ204811.1|BJ204811EST: GGCCGCAAAGCGCAGTCCTGTCAAAGACTTGAAAGTTGTCTTTGTCTTGG GTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTAGATACCT
genomic: GGCCGCAAAGCGCAGTCCTGTCAAAGACTTGAAAGTTGTCTTTGTCTTGGgtatgtgtgg ... tggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgttttcatgcaaacaaacaatgactagtacatcgcgtgattttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
aaacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaatattagctggggtggccatgtttctctgttttttgtataatctgttttcatgcaaacaaacaatgactagtacatcgcgtgattttggaatgcagGTGGACCTGGCAGTGGGAAGGGCACACAGTGTGCCAAGATTGTTGATACCTTTGGATTTGTACACCTAAGTGCGGGGGACTTGTTGAGAGCTGAAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA