Sequence
atgc intronic sequence ATGC exonic sequence...tataatttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctatttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S158_188V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
-tata-atttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctatttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
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ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaact--aggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv19s0014g03380.t01 (Vitis vinifera), 3'ss of exon 2
tataatttaatccttatgtta--atcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctatttaa---ccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
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-----ttttaccaatatgttaggatggcttcgaccattaaattgtctaacttgggctatgcctaaaattgattctcataaatatatttctatattccaatggcagAAAGCAGCCTTTGCGCGTCTATAGCATGGTGAAGTATGCAGCCATAGCCCGGGGAGATGCTGAGATTTTTATGAAGTTTGCAAGAGCTGGATACAAGGAG
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv00s0301g00050.t01 (Vitis vinifera), 3'ss of exon 2
tataatttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatcta--agttagtcgactcttctatttaac--cagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
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aatgat--aatgaaaatggcagatagaagataattaaaa--gaagaaatggaaaacagaaacacatgtgttcattgagtagtttcttttccgtttcaactgcagGAAGCAACCGTTACGTGTATACAGCATGGTGAAGTATGCAGCCATAGCCCGTGGTGATGCAGAGATTTTTATGAAGTTTGCAAGAGCTGGCTACAAGGAA
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ19025 (Selaginella moellendorffii), 3'ss of exon 2
tataatttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctattta-accagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
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--------------------------------------------gtac-gcgaaagtctttctctgcgagcggcaaaaactaacttttgtctccctggcagGAAACGTCCGTTACGGGTCTACAGTATGGCGAAGTATGCAGCAATTGCTCGTGGCGACGCGGAGATCTTCATGAAATTCGCAAGAGCGGGTTACAAGGAGMapped 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|18334029|gb|BJ166045.1|BJ166045EST: CGATGATTTTCAATGGAGAAACATTTANCGAGTTTCATGCTCCTCGTGAG GAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCG
genomic: CGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtct ... atttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgtagacttctaagtcctggatctaagttagtcgactcttctatttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
ctcttctattt CT-rich tract
ttctatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataatttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctatttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - -agctgca