Sequence
atgc intronic sequence ATGC exonic sequence...tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S98_222V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G32040.1 (Glycine max), 3'ss of exon 2
tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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tgtcaaatttgcttttagacttc-tcagaagatatcttatgt-tgtttctagttctacttgccatctctttgttatgact--tttatttttctcatataggcagCAGAGTTCAATGTTCAAGCTGCTCAACAAGGGATTATTTACATTGATGAAGTGGACAAGATAACTAAGAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G13450.1 (Glycine max), 3'ss of exon 5
tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgtta--ctacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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tgaaatggactggttgcaagttgatgaaggaatcataaattaacaaacatagcatcacaaactgtagtctg--aatcaagcattgcatgagtttatttccagGTTGCAGATTATAATGTTGCAGCTGCACAGCAAGGCATTGTTTACATTGATGAAGTTGACAAGATTACTAAAAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G28260.1 (Glycine max), 3'ss of exon 6
----tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaac-ggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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tcctcacctactgttctgtgcaa--agattgttctttttatcttgtttgtagttgcaccttccttccatctcat--tgctatactggttatttttgcta-tacagGCAGCAGATTTCAATGTTGCAGCAGCTCAACAAGGAATAATTTACATTGATGAAGTTGACAAAATAACTAAGAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 6
---tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaac-ggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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cctcatctactgttctgtgcaa--agattgttctttttatcttgtttatagttgcaccttccttccatctcat--tgctatactggttatttttgccataacagGCAGCAGATTTTAATGTTGCAGCAGCTCAACAAGGAATAATTTACATTGATGAAGTTGACAAAATAACGAAGAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G41400.1 (Glycine max), 3'ss of exon 5
tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgtta--ctacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
| | | | | || | | | | | | | | | || || | | ||| | || ||| ||| ||| | |||| ||||| | ||| || ||||| ||||||||||| |||||||||||||||| ||||| || || || |||
tgagatggactggttgcaagttgatgaaagaatcataaattaacaaacatagcatcacaaactgtagtctg--aatcaagcattgcatgagtttatttccagGTTGCAGATTATAATGTTGCAGCTGCACAGCAAGGCATTGTTTACATTGATGAAGTTGACAAGATTACTAAAAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G53350.1 (Arabidopsis thaliana), 3'ss of exon 5
tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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--gtaagcttctaaaacacaaacatttatatttgtatacaac-tataattatttctata---tattgttagtaatgtggggatttgatatctctggacagGTTGCAGATTATAATGTTGCAGCTGCACAGCAAGGGATTGTTTACATTGATGAAGTCGACAAGATAACAAAGAAG
upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv16s0098g01860.t01 (Vitis vinifera), 3'ss of exon 5
---tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaac--ggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
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ggccacaaatcttgaatcgtgtctgtattatgagat-tttgattggaaatgaactat--gctaatcattggagattggtgatcctgatttgttatgttct--cagGTTGCTGACTATAATGTAGCAGCTGCCCAGCAGGGCATCGTTTACATTGATGAAGTTGACAAAATCACAAAGAAGMapped 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|162179889|gb|FC355960.1|FC355960EST: CAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG GAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGAT
genomic: CAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTGgtacgcttct ... gttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGAT
EST:
gi|162247501|gb|FC425067.1|FC425067EST: CAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG GAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGAT
genomic: CAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTGgtacgcttct ... gttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcggtatatctacgaggcattctctcttgctgaacggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
atatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagaaagtgtagaacgaaactaggtcagcatgtgcttgaagcatagcggtatatctacgaggcattctctcttgctgaacggttggatgtgttactacagGAAGCAGAATTTAACGTACTTGCTGCCCAGCAAGGCATCATTTACATTGATGAAGTGGACAAAATCACAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG