Sequence
atgc intronic sequence ATGC exonic sequencegtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S165_107V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
---------------gtgaggaagacggtttctg--ttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagct--tcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
| | || ||||| || | | |||| ||||| |||| || | | || || || | || | || || ||| | | ||| ||| |||| |||||||||||||| ||||||||||| || ||||| ||||||||||||| ||||| ||||||
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgca--actgcctttttctataaaag-aattaactggtgctgattcgctaataatgtgttgttgagtgc-agATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 3'ss of exon 5
------------gtgaggaagacggtttctgttgacgatttttcgtatgcattgt-tgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
|| | || | | | | | | | | | | || | | | | ||| | || | ||| | | | || | | | || | | | |||| |||||||||||||| || |||||||| || || || ||||||||||||| ||||| ||||||
gtatgtgtggctgtaaaaaatatcgcctgtctaggtcaatgtctggatatctaatgtactattgtattgataataagtctgacgtctg-aactcagttaactgtatgctatgatgcagATATTCCGCAAGGAGCCATTCTTCTATGGTCATGATAACCATGATCAACTTGTCAAGATCGCAAAG
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
---------------------gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagcttccta--tagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
| | | ||| ||| | | | |||| |||| ||| | || || || | || | | || ||| || |||| || |||||||| || || || |||||||| ||||| |||| |||||||||||||||||||||
gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgc-agATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgttta-caatcaaccagcttcctatagacctgatagtcgatcattgggtgtt--agATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
|| | ||| | | | | || ||| | ||| |||| ||| | | | | || || | | || | | | | || || | |||| || |||||||| || || || |||||||| ||||| |||| |||||||||||||||||||||
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaat-actattggacacgatggggattgacattttgtcaagtgcttcagtggttttttacccatat-atgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------gtgaggaagacggtt-tctgttgacgatttttcg--tatgcattgttgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgtt---agATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
|| | | || | |||| | |||| | |||| | | ||| | || || || | || ||| | || | |||| |||| ||||||||||||||||| || |||||||| ||||| ||||||||| | || || ||||| |||
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttac---cattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 5
gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgtt--agATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
| || ||| || | | || | || ||| | | | | ||||| || || | || || | | ||| | | ||||||||||||||||||| |||||||| || || || |||||||||||||| || || || || |||
-ggtggcagatggcaa-----ggtggttccaattttgacaccatgcaaaggtatgtggtgtcaactc-tttactgtgatgcttattttaaaagcttgtgccatacagATTTTCCGCAAGGAGCCATTTTTCTACGGGCATGATAATTATGATCAACTGGTTAAAATAGCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
acctgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG