Sequence
atgc intronic sequence ATGC exonic sequencegtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S121_22V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 5
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
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-------------------------------------------------gtaagtcagttaatattgcttgttaccgtcattcattttgctggtggttc-tcatgcataaa-----atttctcatgagggatcctttgttcatgt--------cagCCGAAGTGGAGTGACCTTGATGTCAACCAGCATGTGAACAATGTGAAGTATATTGGTTGGATACTTGAG
upper sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G017382_T01 (Zea mays), 3'ss of exon 4
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG-------------------------------
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---------------------------------------------------------------------gtaaggaggagcagaccagaacacctctcgtcccgtctggttggaccgctctcaactgaaaaacttgttcccccctt-------cagCCCAGGTGGAGTGACATGGACGTCAACCAGCACGTGAACAACGTCAAGTACATCGGTTGGATCCTCGAGAGCGTGCCGCTGGACGTGCTGGAGGATTACC
upper sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG-------------------------------
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--------------------------------------------------gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagctt--gtaagactctctaat-------ggcttggtaatgaacatttt-------cagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
upper sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ13354 (Selaginella moellendorffii), 3'ss of exon 4
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
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-------------------------------------------------------------------------gtgagtatccatctcactttcctttctctttcctg-------cgctttttttaaagtatc-atcttt-gcattt-----gcagCCAAGGCATGGAGACTTGGACATGAACCAGCACGTGAACAACGTAAAGTACATCGGATGGATGCTCGAG
upper sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11934 (Selaginella moellendorffii), 3'ss of exon 4
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
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-------------------------------------------------------------------------gtgagtatccatctcactttcctttctctttcctg-------cgctttttttaaagtatc-atcttt-gcattt-----gcagCCAAGGCATGGAGATTTGGACATGAACCAGCACGTGAACAACGTAAAATACATCGGATGGATGCTCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
ttctgat putative branch site (score: 3)
tctcccgtatttct CT-rich tract
aattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG