Sequence
atgc intronic sequence ATGC exonic sequence...agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S2_300V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 2
------agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
|| | | || | | || | || | ||| | | || ||| || | |||| | || |||| || | |||| |||||| | |||| ||||||| | ||||| || || ||| || | || |||||||| ||||||||||| |||||||| |||||||| | || | ||
aaaatgcttgttgctgtttcagaagaccttgctttattgcaaggatggtcacttaat--cttacttattgggtcttaatatca----catttcttcttacctgcagCTTCGCAAACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 2
agtgaggtttcccaaggttgcactatttaaatgtatgga-gcatgaagaaagggtttagttggtacatcttgctgaca-agtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
|||| | || | | || | ||| || | | | || | | || | | | || | ||| | || ||||||| ||| | |||| ||||||| | ||||| || |||||| || |||| |||||||||||||||||||| ||||| || |||||||| | || |||||
--ctgggttctcttagttaagaaaatcgggactgatgttcatttgtgacatgagattgtatactgtttcatatgatctcactgttctttttatatttcgcagCCTCACAAACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 3
----------agtgaggtttcccaaggttgcactat---ttaaatgtatggagcatgaagaaagggt---ttagttggtacatct---tgctgacaagtg-cattgtttttccatca-----------------cagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| | || | || |||||| || | ||| | ||| || | ||| ||| ||| | | | | || | ||||| || || |||| ||||| || |||||||| ||| | ||||| || || || || | || |||||||||||||||||||| ||||||||||||||||| | ||||| ||
gtgagtgtttgttaattttaactttaatttcactattctttgttcctttggtgaatgctgagtttttatgttacttgttacttttatctatttgtggttgtctttgttcttgaattttgagtgttggctgtctccagCATCGCAGTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
---------------------------------------------------------agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggt-acatcttgctga----caagtgc--attgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| |||| ||| ||| || | | | | || || |||| | | ||| || | | | | | |||| |||| ||||| || |||||||||||| | |||||||| || || || | || ||||||||||| |||||||| ||||| ||||||||||| | ||||| ||
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgc---tgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
agtgaggtttcccaag---gttgcactatttaaatgtatggagca-tgaagaaagggtttagttggtacatcttgctgacaagtgcattg--tttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| |||| | |||| | | || | || | || || || | || | ||||||| | ||| ||||||||| |||| |||||||| |||||||| ||| | ||||| || ||||| || | || ||||||||||| |||||||| |||||||| || ||||| ||||||| ||
----aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtga-ttgctgatgttttgtttgtgtttttccatt-cagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 3
agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatca--cagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
|| |||| |||| | ||| || ||| || ||||| | || | ||| | | | | | | ||| | || ||||||| ||||| |||||||| ||| | |||||||| ||||| || | || |||||||||||||| ||||| ||||| || || ||||| ||||||| ||
ttctagttttcattctgttg-gccatt-aattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------agtgaggtttcccaaggttgcactatt-----taaatgtatggagca-tgaagaaagggtttagttg-gtacatcttgctgacaagtgcattgtttttccatca--cagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| | |||| | || || | ||| | || | || | || || | |||| || | ||| | | | | | | ||| | || ||||||| ||||| |||||||| ||| | |||||||| ||||| || | || |||||||||||||| ||||| ||||| || || ||||| ||||||| ||
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaat-tgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 3
agtgaggtttcccaaggttgcactatttaaatgtatggagca--tgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| | | | || || | | |||| || | || | || | | | || | || | | || || | | |||| || ||||| |||||||||||| | ||||| || || ||| || | ||||||||||||||||| ||||| ||||| ||||||||||| ||||| | ||
-ctcatctgatcaaaactttgaaccatgaaatagggagatcttttggactttggatgcattgcctatttgttttcattgtcttccttccttattt-ttgcagCATCACAATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 2
agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| ||| |||| || || | | || || ||| | || || |||| || || ||||||||||||||| |||||||||| || || | |||| || |||||||| ||||| || ||||||||||| ||||| ||||||| ||
----------------------------------------------gtaagtgtttc-ttcgtgtttgtctct-acttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG
upper sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ04804 (Selaginella moellendorffii), 3'ss of exon 2
agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
| ||| |||| || || | | || || ||| | || || |||| || || ||||||||||||||| ||||||||||||| || | |||| || |||||||| ||||| || ||||||||||| ||||| ||||||| ||
----------------------------------------------gtaagtgtttc-ttcgtgtttgtctct-acttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
tgctgac putative branch site (score: 2)
ttgtttttcc putative PPT
attgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT