Sequence
atgc intronic sequence ATGC exonic sequencegtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S3_299V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G63440.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG-----------
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-------------------------------------------------------gtaaaacatagtattatggcacaaaatctat-tttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGGTACCAAATCA
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
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-------------------------------------------------------gtaaaacatagtattatggcacaaaatctat-tttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ36938 (Selaginella moellendorffii), 3'ss of exon 4
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcac-agGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
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----------------------------------------------------------------------------------gtgagtgttttcgttttcttccttttg--agtatca-----gacctccttt-----ggtgcctgctccagGAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCAAACAACGAACTTCTGGAGTACATGGCAAAGMapped 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|37852757|gb|BJ610765.1|BJ610765EST: CCAGGTTGCTATTGAAGTTGAGGATCGCGCACAACGTTCACAAATTTCAC GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTG
genomic: CCAGGTTGCTATTGAAGTTGAGGATCGCGCACAACGTTCACAAATTACACgtatgctgtc ... atctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
cattaac putative branch site (score: 2)
aattatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT