Sequence
atgc intronic sequence ATGC exonic sequencegtactaatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatgttaatattattcttgcaaactatagccaggtggacgtcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTGCAAGACATGGAAGGA
Basic information
species | Physcomitrella patens |
transcript | PP1S61_196V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S61_196V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv04s0008g01870.t01 (Vitis vinifera), 3'ss of exon 2
gtactaatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatgttaatattattcttgcaaactatagccaggtggacgtcacatggtgggaatgacgacctaacttggcaaaattttggtgct-acacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTGCAAGACATGGAAGGA
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------------------------------------------ttaccttaaaagtttaa-gcatataggatttgggtccagtatatcatgctattttacatgtggtttgattgttttttttttttt------ttttgatccttgtttagGTGGTCTTTGATTGCTGGAAGGTTACCGGGTCGAACAGACAATGAGATCAAGAACTACTGGAATTCTCATTTAAGCAAGAAGACAAAGCAGAAGGAGAAA
upper sequence: PP1S61_196V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0117g00200.t01 (Vitis vinifera), 3'ss of exon 2
gtactaatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatgttaatattattcttgcaaactatagccaggtggacgtcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCT-GCAAGACATGGAAGGA
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--------------------------------------------gtaagaatttctcaggattcacctt-ttctcg------atagccaaacagcttttagac--tgaaactgaaagtcgaaatgtttgaaatcc-gacgt----cagGTGGTCGCTGATCGCGGGGCGATTGCCCGGAAGAACAGACAACGAGATCAAAAACCACTGGAACACTCACATCAGGCGGAAGCTCATCAGTGGCGGAATC-
upper sequence: PP1S61_196V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ10825 (Selaginella moellendorffii), 3'ss of exon 2
---gtac-taatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatg----ttaatattattcttgcaaactatagccaggtggacg--tcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTG-CAAGACATGGAAGGA
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gtgatacaccacccaccaattctgtcccgattcaatccgatgcggtggcggcagcgaaatcggtgcgcttgggcaccgtgatcgcgccgcgctcgcatctgggctctttgcaaaatcgtgttttgatccccaattccccgg-ttttgatga-atgcagGTGGTCGCTCATCGCGGCTCGGATGCCCGGGCGGACAGACAACGAGATCAAAAACTACTGGAACACGCACCTGAGCAAGAAGCTGGCCAGCCGGGGATTG-
upper sequence: PP1S61_196V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26117 (Selaginella moellendorffii), 3'ss of exon 2
---gtac-taatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatg----ttaatattattcttgcaaactatagccaggtggacg--tcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTG-CAAGACATGGAAGGA
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gtgatacaccacccaccaattctgtcccgattcaatccgatgcggtggcggcagcgaaatcggtgcgcttgggcaccgtgatcgcgccgcgctcgcatctgggctctttgcaaaatcgtgttttgatccccaattccccgg-ttttgatga-atgcagGTGGTCGCTCATCGCAGCTCGGATGCCCGGGCGGACAGACAACGAGATCAAAAACTACTGGAACACGCACCTGAGCAAGAAGCTGGCCAGCCGGGGATTG-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|18353128|gb|BJ185183.1|BJ185183EST: CCTGATGAGGACGAGCTGATCATCAAGTTGCACTCTCTTCTAGGAAACAA GTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAA
genomic: CCTGATGAGGACGAGCTGATCATCAAGTTGCACTCTCTTCTAGGAAACAAgtactaatct ... tgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacgtcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTGCAAGACATGGAAGGA
acctaac putative branch site (score: 2)
aaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaatctctcgaatctctatgttgttattgttatcttattttttttactatttcgatgttaatattattcttgcaaactatagccaggtggacgtcacatggtgggaatgacgacctaacttggcaaaattttggtgctacacagGTGGTCGCTGATTGCTGGCCGCATTCCTGGACGAACAGACAATGAGATCAAAAACTACTGGAACTCTCGTCTGAAGCGCAATCTGCAAGACATGGAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG