Sequence
atgc intronic sequence ATGC exonic sequence...atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
Basic information
species | Physcomitrella patens |
transcript | PP1S448_20V6.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
------atgcctgtttgttacttgtggtggattctcaat-ctgactacatttctggctctgctctgttgtcgaagt--tgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
| | |||||| | | | || || | |||| | ||||| | |||| || ||| | | |||| || || | || | |||||||||| ||||| ||||||||||||||||| || || | ||||| || || ||||| ||||||||||| || | | | ||||||||||| |
gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgtt-----ttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 6
atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttg----tcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
| | |||| || | || | | | || | | | || || ||| | ||| ||| | | || || |||||||||| |||| ||||||| ||||||||| | || || | |||||| || || || || |||||||||||||| | | ||||||||||| |
gtaaattattgtaacagatcctgttgtgttttttcatcttctagtttagcactatgtatttgacaaccaaaggctaagtgttttactctttttttttatacaagGTGGTATGCCAAGAGATTTTTACATCCTGATATTGTTGCCCCGTATGACTACATATTTATCTGGGATGAGGATCTAAGTGTACAACATTTCAATGCAGAG
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
---atgcctgtttgt-tacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
| ||||| || ||| ||| || | | | | | | | || ||| || | || | ||| | | ||| | |||||||||| |||| |||| ||||||||||| | |||||| ||||| || || ||||||||||||||||| |||| | ||||| ||||| |
gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtt-------tgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 7
-atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgatt-ttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
| | | || | | ||| |||||| || | | || | || ||| | || | || ||||| | | | || |||||||| | ||||||||| | |||||||| | || || | ||||||||||||||||| |||||||||||||||| || || || || ||
gttagtggcctctttactaagcaggaacgccaatctt-cttcctagtaggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
atgcctgtttgttacttgtggtggattct-caatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgatttta----ggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
|| | || | | | || ||| | | | || | | | || | | || | ||| | | | |||| |||||||||| || | ||| ||||||||||| | | |||| ||||||||||| |||||||||||||| ||||||| | | ||| | ||
-----------------gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
-----atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaact-gattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
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gtaagaaatctgaaatgtaggtcagcacgatatac--tctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGATMapped 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|162177786|gb|FC354620.1|FC354620EST: GAATGGTCTCAAAACGCCATTCATATAAGTATTCGTAAGCAAGCCAAGTG GTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATA
genomic: GAATGGTCTCAAAACGCCATTCATATAAGTATTCGTAAGCAAGCCAAGTGgtatgttccc ... gcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggctctgctctgttgtcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
aactgat putative branch site (score: 3)
tgatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT