Sequence
atgc intronic sequence ATGC exonic sequence...ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtatttattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
Basic information
| species | Physcomitrella patens |
| transcript | PP1S164_33V6.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g37920.1 (Oryza sativa), 3'ss of exon 1
ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtatttattgtagcacatacttcgataagattaatgttggtttgctctgacatg---cagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
|| | || | || | || | | ||| || ||| || | ||| | | | | |||| ||| | ||| | || ||| |||||| | || || || ||||||||||| ||||| || |||||||| |||||||| || ||||| || || |||||||| || | || || |
--tagcttggatgtg-tagtgctcgatcgatcgatcgatcgatcgatctggtgtcgtttacttgtttgtgcgatttatgcgtgcatgcatcggtttgtatcagAGAAGGCGAACTTCGGGGAGCAGGAGTGGTATTTCTTCAGCCCGAGGGACCGCAAGTACCCGAACGGGGCGCGGCCGAACCGGGCGGCGACGTCGGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G26740.1 (Glycine max), 3'ss of exon 1
ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtat---ttattgtagcacatacttcgataagattaatg----ttggtttgctctgacat----gcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
|| | | || || | ||| | | || |||| | | | | |||||| ||| || ||||| | || ||| ||||| || || || ||||||||| || |||||||| || |||||||||||||||||||| || | || ||| |||| ||||||||||| |
----------ttcgtgtgcactagaagagttttaattttcttttcttctttttttgtggtgtgtgatgtgg-aagattgatgtttttttgtttgttgtggttcttcaacagCTAAGGCCGCGTTTGGGGAGAAAGAGTGGTACTTCTTCAGTCCTAGAGACCGGAAGTACCCAAATGGAGCGAGGCCAAACAGGGCAGCAGCTTCAGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G07700.1 (Glycine max), 3'ss of exon 1
-ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtatttattgtagcacat--acttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
| | | ||| || || | | || ||| | | | ||| | | || | | | | || ||| || | | ||| ||||| || || || ||||||||| || |||||||| || |||||||||||||||||||| || | || ||| |||| ||||||||||| |
cactagaagagttttaattttcttaattttcttctttttgtatggagtgtgatgtggaagattgatgtttttttgtttggtgtacgtggatcttca---acagCTAAGGCCGAGTTTGGGGAGAAAGAGTGGTACTTCTTCAGTCCTAGAGACCGGAAGTACCCAAATGGAGCAAGGCCAAACAGGGCAGCAGCTTCAGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G35630.1 (Glycine max), 3'ss of exon 1
ccaggcggtgttgcgat----atttctgggtagattgagtttaagatgtatt-tattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
|| |||| || || || | | |||| ||| || ||||||| |||| | | || | || || | || |||||| || || || |||||| || |||||||| || |||||||| ||| |||||||||||||||||| | || ||||| || | | || || |
---accgaaattgcaatcgcggaccctttttaaaatc--cttaacatgaatggtattgtattacatctcctaacacacttgttattaacttaccatggaatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTAGTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACTGTGTCTGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G07620.1 (Glycine max), 3'ss of exon 1
-----------------------------------------ccaggcggtgttgcg--atatttctggg-tagattgagt--ttaagatgtatttattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
|| || | ||||||| | | |||| | | | || ||||| ||| | | ||| || || || || |||| | | ||| || |||| ||| || || ||||||||| |||||||| |||||||| |||| |||||||||||| | | || ||| | ||||| |||| || |
gtatgcaacttcatcacaccccaacttttcttttcctcctttcatgcaaacccacttcatatttccatgcttaattgcttaccttatatttattttttggatccaatattttcatt---tttgactttttttgtgtttttttttagGTAAAGCAACTTTTGGTGATCAAGAGTGGTACTTTTTCAGCCCAAGGGATAGGAAATACCCAAATGGGTCAAGGCCTAACAGAGCTGCTTCTTCTGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G31220.1 (Glycine max), 3'ss of exon 1
ccaggcggtgttgcgatatttctgggtagattgagtttaag---atgtatttattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
| | | | | | | ||| || | | | | | || |||| || | | | | || || ||| | | | ||| || |||| ||| || || ||||||||| |||||||| |||||||| | || ||||||||||||||| | ||||| | ||||| |||| || |
caacgtgatactagaaaattcacggtgaaaccaaatacacatttgtgaatttgttttgat---tgtaatgttttttcccattttctttttttgggtttcgtagGTAAAGCAACTTTTGGTGAGCAAGAGTGGTACTTTTTCAGCCCAAGGGATAGAAAATACCCAAATGGGGCTAGGCCCAATAGAGCTGCTACTTCTGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
ccaggcggtgt-tgcgatatttctgggtagattgagtttaagatgtatt-tattgtagcacatacttcgataagattaatgttggtttgctctgacatg-cagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
| | | ||| |||| | | || | | || | || || | | || | | | || | ||| | || | | | ||| ||||| | || || || ||| |||||||| |||||||| || ||||| |||||||||||||| || | || ||| |||| || |||||||| |
--aaatattatatgcactattattactcaagaagataaaatatcatgttatgttagaggctagagttagtgatggtttgt-ttgttgtggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
upper sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0014g03290.t01 (Vitis vinifera), 3'ss of exon 1
ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtatttattgtagcacatacttcgataagatt---aatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
| | ||||| | || | | | || | || | || ||| | || | || ||| || || |||||| || || || || ||||| ||||||||| ||||||||||| || || |||||||||||||||||| | ||||||| ||| ||| | || || |
-----------------------gtgagtattgattcgaaaacctgcgttttctgcttca-atttggatttgtttctgatcatttatttact-tgttctgcagGTAAAGCTATATTTGGAGAGAAAGAGTGGTACTTTTTCAGTCCCAGAGATCGGAAGTACCCAAATGGGTCCAGACCCAATAGGGTTGCTGGGTCTGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
ctctgac putative branch site (score: 3)
tttgctct CT-rich tract
ataagattaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaggcggtgttgcgatatttctgggtagattgagtttaagatgtatttattgtagcacatacttcgataagattaatgttggtttgctctgacatgcagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatac
