Sequence
atgc intronic sequence ATGC exonic sequenceATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaagcagcaaccaaaattaagcctcaaacagccaagtctgatcttttgcacgcatgctctacgtatcttcatctaaggagtaaattcgttagtg...
Basic information
species | Physcomitrella patens |
transcript | PP1S10_296V6.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G072865_T03 (Zea mays), 5'ss of exon 3
ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagt-------gaagcagcaacc--aaaattaagcctcaaacagccaagtc-------tgatcttttgcacgcatgctctacgta-------tcttca-----tctaaggagtaaattcgtt--agtg-----------
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--ATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGGCAAAAGAAGAGCTTGAAGAAATTGTGGTatggtcgtatggatcctacagtttgacagtagcacttgcagcaatcaaataagggaaataagctggtccatacatattttttgttcaggagttcttaaggaacccagaaagatatattcgtctcggtgctcgccctcct
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G163193_T02 (Zea mays), 5'ss of exon 3
-ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaagcagcaacc--aaaattaagcctcaaacagccaagtctgatcttttgcacgcatgctctacgtatcttcatctaaggagtaaattcgttagtg
| | || || ||| || || | | | ||| ||||| ||||| || || || || || |||||||||||||||||||||||||| ||| | || | ||| | | | | | | | || |||| | | | | || || || | ||| || | | |
TAATTCTGGTAGAGCAAAAGTTTCTGAAAGT-ACAGATATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGGCAAAAGAAGAGCTTGAAGAAATTGTGgtatg-gatcctacaatttgacagtaatacttgcagcaaccaaataagggaaat---aagc-tggtccatatatttttttgttcag----------------
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G072865_T02 (Zea mays), 5'ss of exon 3
-ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgta-agtgaagcagcaaccaaaattaagcctcaaacagccaagtctgatcttttgcacgcatgctctacgtatcttcatctaaggagtaaattcgttagtg
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TAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGA-TATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGGCAAAAGAAGAGCTTGAAGAAATTGTGgtatggtcgtatggatcctacagtttgac----agtagc--acttgcagcaatcaaataagggaaataagctggtccatacatattttttgttcag-----
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G072865_T04 (Zea mays), 5'ss of exon 3
ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagt-------gaagcagcaacc--aaaattaagcctcaaacagccaagtc-------tgatcttttgcacgcatgctctacgta-------tcttca-----tctaaggagtaaattcgtt--agtg-----------
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AATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGA-TATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGGCAAAAGAAGAGCTTGAAGAAATTGTGGtatggtcgtatggatcctacagtttgacagtagcacttgcagcaatcaaataagggaaataagctggtccatacatattttttgttcaggagttcttaaggaacccagaaagatatattcgtctcggtgctcgccctcct
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTATCGGGA-GGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaagcagcaaccaaaattaagcctca--------aacagccaagtctgatcttttgcacgcatgctctac---gtatcttcatctaaggagtaaattcgttagtg---
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-TGGTCCTGATGGGGGAAAAGTCTCTGGTGGAGGTGAAACAATCACTTTTGCGGATGTTGCAGGTGTTGATGAAGCAAAGGAAGAGCTAGAAGAAATCGTGgtaggtttttcagtccttaaagacgctgcacatgcttattgatgatcagattgtttttcatagctttattctcggtttggtaattgtcttttacacatcggttaatcaatgcag
upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ33021 (Selaginella moellendorffii), 5'ss of exon 3
ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaagcagcaaccaaaattaagcctcaaacagccaagtctgatcttttgcacgcatgctctacgtatcttcatctaaggagtaaattcgttagtg
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AAACAAAAAGGACAGCAAAGACCGCGATCGAGAGGGTCCTATTATGTTTGCAGACGTTGCAGGGGTTGATGAAGCCAAGGAAGAGCTCGAAGAAATAGTGgtacgtgcttccgt--cttacgaaaagcatttgacactcacaaccgattgtag-----------------------------------------------Mapped 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|162254897|gb|FC431082.1|FC431082EST: CGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTT GAATTTCTTAAACACCCTGAGCGGTATTCAAGGCTCGGAGCCAGGCCACCA
genomic: CGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaag ... cctattgtagGAATTTCTTAAACACCCTGAGCGGTATTCAAGGCTCGGAGCCAGGCCACCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTATCGGGAGGTGGCAAGGATCAAGGTGTTGGGGGTCCAATTATGTTTGCGGATGTTGCAGGTGTGGACGAAGCAAAAGAAGAGCTTGAAGAAATTGTTgtaagtgaagcagcaaccaaaattaagcctcaaacagccaagtctgatcttttgcacgcatgctctacgtatcttcatctaaggagtaaattcgttagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaaa