Sequence
atgc intronic sequence ATGC exonic sequence...tgtcttcactccaacgaaagcataggggcgatgctggtctcgcgtatgcggaggttggttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S79_54V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 9
tgtcttcactccaacgaaagcataggggcgatgctggtctcgcgtatg------cggaggttggttacatttcagctgaatgtttctgatcc-atcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
|| | | | | || || || | || | | | ||||| || | | | | | ||| | || | | | ||| | || || ||||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| |||| | || ||||| |||
------tgctttgagggttgagttaggctcattttgttttcatttgtaaccatttcaaagttgggta-acctgaaaaaattctttattttctgaatccatcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGA
upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 9
tgtcttcactccaacgaaagcataggggcgatgctggtctcgcgtatg------cggaggttggttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
|| | | | | || || | | || | | || ||||| || | | | || | | | | ||| | || || ||||||||||||| ||| ||| ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| | || | || ||||| |||
------tgctttgagggtcgagttaggctcatttttttttcatttgtaaccattttgaagttgggtaacctgaaaaagttctttatttgctgaatccatcctacagGTGTTGTATGACTATGAAGACAGAATAAATCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCTGGCTTAGCAGTTGCACTGA
upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------tgtcttc--actccaacgaaagca-taggggcgatgctggtctcgcgtatgcggaggttggt-tacatttcagctgaatgtttctgatccatcctgc--tgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
| || | | || | || |||| | | || | | | || | |||| | || ||| || | | | || ||| | || || | || || |||||||| |||||||| || |||||||| || ||||| |||||||| |||||||||||||| ||| | || | |||||||| ||||
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttcctacttga--gttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------tgtcttcactccaacga-aagcataggggcgatgctggtctcgcgtat-gcggaggtt--ggttacatt-tcagctgaatgtttctgatccatcctgc-----tgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
| || | |||||| | || || || | || | | | || || ||||| ||| | | | | || || || |||| || |||| || ||||||||||||||||| ||| ||||| ||||| ||||| ||||| || |||||||| ||||| ||||| || | |||||||| ||||
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcat-actccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------tgtcttcactccaacgaaagcataggggc--gatgctggtctcgcgtatgcggaggttg----gttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
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gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcct-actccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata--tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAMapped 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|67698707|gb|BJ958940.1|BJ958940EST: GAGACAACCAAGAAGGGTGAACAG ATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
genomic: GAGACAAACAAGAAGGGTGAACAGgtatttcaga ... tgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
EST:
gi|67575248|gb|BJ948072.1|BJ948072EST: TGATCTTCTACCGCAAAGGGTTGAAGGAGACAAACAAGAAGGGTGAACAG ATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
genomic: TGATCTTCTACCGCAAAGGGTTGAAGGAGACAAACAAGAAGGGTGAACAGgtatttcaga ... tgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
EST:
gi|162179834|gb|FC355905.1|FC355905EST: CGCAAAGGG-TGAAGGGAGACAAACAAGAAGGGTGAACAG ATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
genomic: CGCAAAGGGTTGAA-GGAGACAAACAAGAAGGGTGAACAGgtatttcaga ... tgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcggaggttggttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
ttctgat putative branch site (score: 3)
tccatcct CT-rich tract
ttacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcttcactccaacgaaagcataggggcgatgctggtctcgcgtatgcggaggttggttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT