Sequence
atgc intronic sequence ATGC exonic sequence...cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S9_129V6.2 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 10
cctttacttgtaactttacttgtgggtagggagcctatatatgc-gtctgtga---aactgccataatatgcttacatcctttc-tgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
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----tagctaaggcctgaggtgccatcaatga-ctgataattgttgttttagactcagttctgatgttgtggttatttatttttgcacatgtcgaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
upper sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgca-------atttatttgag--------tgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
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------gtggcgacatcaatcaggtgtca----cttgtat-tacgtccatgaatcc----taacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
upper sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
--cctttacttgtaactttacttgtgggtagggagcctat-atatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
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gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaattt---agattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
upper sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
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-------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctag------ttct-cgatcgatgc-aacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
tgcttac putative branch site (score: 2)
tttattt putative PPT
aatttatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
