Sequence
atgc intronic sequence ATGC exonic sequencegtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
Basic information
species | Physcomitrella patens |
transcript | PP1S147_62V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
----gtgcattctaatatccgacttgaatttcaaaatcta---gtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctga--taatgtggtgg-atttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
||| || | | | || | || || |||| || | || | | || | | | | | | || | ||| || | || | || || | | | | | ||| || | | |||||| | | || | |||||| ||||||||||| ||||| || || ||||| |||||||| ||||| || || || | ||||| || ||||||||||| || || || ||||||||
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaa--gtgtttggttcagtgt--ccatccacttttgtttatcagatcatttattg--aagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
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-------------------------------gttctgtctaaaaaaccttgc-------tctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttct--------tctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 9
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcat--gattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttc--agGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
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----------------------------------------------gtttgcttttatcttggaatatttccaaaagattcagattaaattaataactgctttaaagtagaag--caacatgctatgtaaaatgactttttccaccttttggttttttgtgcttcaattatcttctcagGTTCCAAGAAAGTTTACTAGCAAGATTGAGGGGAAGATGGGTTATGAAGATTTTGTTTACTTCATGCTGTCAGAGGAGGATAAGTCATCAGAGCCTGGTC
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 8
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
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---------------------------------------------------------------------------------------gtaacgtttggcactttccaaaagaatgatctttcgagttctcgg-----ttcctctaatgtgcttcatgtt-tttagtatttgtcagGTTCCAAGAAAGTTTACGAGTTCCGTGGAAGGAAAGATGGGTTACGAGGACTTTGTGTGGTTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 8
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
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---------------------------------------------------------------------------------------gtaacgtttggcactttccaaaagaatgatcgttcgagttctcgg-----ttcctctaatgtgctttatgtt-tttagtatttgtcagGTTCCAAGAAAGTTTACGAGTTCCGTGGAAGGAAAGATGGGTTACGAGGACTTTGTGTGGTTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCTMapped 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|162193203|gb|FC369963.1|FC369963EST: ATGGAAATCATGCTCTCACCTACCGAATCGTGGAGCGTATCTTTTCCCAG GTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGAC
genomic: ATGGAAATCATGCTCTCACCTACCGAATCGTGGAGCGTATCTTTTCCCAGgtgcattcta ... tggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
ttctgat putative branch site (score: 3)
aaaaagaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA