Sequence
atgc intronic sequence ATGC exonic sequencegttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S53_93V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S53_93V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g24550.1 (Oryza sativa), 3'ss of exon 2
gttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
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----------------gttcgtgctctgg----attccgctcgtacggtgaaatggaatggttaattcttttttcttttttttttctg--ctagttttg-----ctcggaagtttgattgcttctg-----tttaaatttgtttcagACGGTAGCTATGAAGTTTATCCTTAAGCATGGGAAGACTGACAAAGATATACATAATCTAAGGCAGGAGATTGAG
upper sequence: PP1S53_93V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 1
gttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
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------------------------------------------------gtacttgttgcaattcccttctcttgccttttgagt--gaattggaggtggtttgacttgcttcatccttatcttagtgctgtttta-attgatctcagACTGTTGCAATGAAATTTATTCTCAAGCATGGGAAAAGTGAGAAGGACATTCAGAATCTAAGACAGGAAATTGAG
upper sequence: PP1S53_93V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37043 (Selaginella moellendorffii), 3'ss of exon 1
gttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG---
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-------------------------------------------------------------------------------------------------------tttggttttcttgcttgcccctgatcgatcg--atcgac-
upper sequence: PP1S53_93V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ33693 (Selaginella moellendorffii), 3'ss of exon 1
gttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatct-attgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
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----------------------------------------------------------------------------------------gttctgtgagctacattttgtttttcttgcttgcccctgatcgatcg--atcgac--cagACTGTCGCCATGAAATTTATTCTCAAGCACGGCAAGAGCGACAAGGACATCGAGAATTTGCGGCAAGAGATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
aatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaccttctaccacttgtatcatgtgagcatgtcacttaagcagagatcctcaatggttcacgcggttactcttttacatccgggttttgcttcgaatatttcgtcgatctattgacttgcgataactccacattgattgcagACGGTTGCAATGAAGTTTATACTCAAGCATGGCAAGAGCGACAAGGATATTGATAATCTCAGACAGGAGATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT