Sequence
atgc intronic sequence ATGC exonic sequencegcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatagatgacaaaaatatttgctccatgctggtattattaaatttatcctgtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S7_163V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S7_163V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
------------gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatag-atgacaaaaatatttgctccatgctggtattattaaattt-atcctgtacaccacatcctgattctctgcacttgcatgatgttct------atggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
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gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
upper sequence: PP1S7_163V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 3
gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatagatgacaaaaatatttgctccatgctggtattattaaatttatcctgtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggac-agCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
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---------------------------------------------------tattaagatctctctctctctctctctctctcttcctcttcattttct-cattgtcttctatttttctgatgcatttttaacttctattgcaatgggccagCTGAAACTGTAATATACCGAATATTTTACTACATGAATAGATCTGGGAATGGTCAACTTACCCTCAGAGAGCTAAAACGTGGGAACTTAATTGCTGCAAT
upper sequence: PP1S7_163V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 6
gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatagatgacaaaaatatttgctccatgctggtattattaaatttatcct-gtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
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----------------------------------------------------------------gttggttgatttttttagtgttgtttttgttgtcgctcagatcattct--ttttctttgtttgc-ttttgttcttt--ttgttcgcagCCGAGACAGTAATGTACAGGATATTCTACCATGTAAATAGATCTGGAAATGGAAGGCTATTGCTAAGAGAGTTGAGAAGAAGCAACCTTGTTGCAGCACT
upper sequence: PP1S7_163V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 6
gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatagatgacaaaaatatttgctccatgctggtattattaaatttatcctgtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
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------------------------------------------------------------gttggctgatttgtttagtttttttttttgttgtc--gctcaaatcattct--ttttctttgtttgc-ttttgttcttt--ttgttcgcagCCGAGACAGTAATGTACAGGATATTCTACCATGTAAATAGATCTGGAAATGGAAGGCTATTGCTAAGAGAGTTGAGAAGAAGCAACCTTGTTGCAGCACTMapped 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|162155853|gb|FC332402.1|FC332402EST: TCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATG CTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATG
genomic: TCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATGgcatgaattc ... tggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
tcctgat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatagatgacaaaaatatttgctccatgctggtattattaaatttatcctgtacaccacatcctgattctctgcacttgcatgatgttctatggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT