Sequence
atgc intronic sequence ATGC exonic sequencegtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttggtgggcggtgtaatggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S195_46V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttggtgggcggtgtaatggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
|| | | || | ||| | ||| | || ||| | ||| || | || | | ||| | ||||| || |||||| | |||| |||| |||||||||||||| ||||| || ||| ||||||| |||||||| || ||||| || ||||| ||||
----------------------------------------------gtactgcacatttgaccagaaaaatcctagtcttggactctgaaat------tgcttgcttactcttttattctctgcaatgcagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttggtgggcggtgtaa-tggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
| ||| || |||| | || | || | ||| | ||| | ||| | || | | | | | ||| | ||||| || || ||| |||||| |||| |||||||||||||| ||||| || || ||||||||||||||||| || ||||| |||||||| ||||
-----------------------------------------------------gtactgtcttgcttcctgccagacgatgt-cattgtgggttgaaattgtttacttactgtttcttttctgtg-atgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttggtgg-gcggtgtaatg-gaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
| ||| || ||| || || || ||| | ||| | |||| ||| | ||| | | ||| | ||||| || || ||| |||||| |||| |||||||||||||| ||||| || || ||||| ||||||||||| || ||||| || ||||| ||||
-----------------------------------------------------gtactgtcttgtttcccgccagatgatgtcattgtgggttctgaaattgtttatttactgctgctttttctgtgatgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttctt-ccctcttggtgggcggt-gtaatggaaggtacttatacctggcttggtgttcgggcgtc--cagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
||| || ||| ||| | | ||||| | | |||||| | | || | | ||| || ||| | ||| | | |||| | | ||| | || | | || | ||| |||| |||||||||||||| |||| |||| || || || ||||| || || |||||| ||||||||||||| || |||||||| |||||||| ||||
gtatagtttctgtt--aatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttg---gtgggcggtgtaatggaaggtacttatacctggcttggtgttc----gggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
| || ||| | | || || | | | | || | |||| | | ||| ||| || | | | | | | ||| | || || | |||||| | | |||||||| |||||||||||||| |||| |||| || || || ||||| || || || ||| |||||||||||||| | || ||||| |||||||| ||||
-------gtatgtctgcattttatt--attcccttttgaaagtattatgttttgtctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
gtaggacttgcgttccaattcaactggatgccatggttgcaattttt-tattttatttt-gttttacttcttc--cctcttggtgggcggtgtaatggaaggt-acttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
||| || || | || | | | || || || ||| | | ||||||||| || || | | | | ||| | | || ||| | | ||| | | || ||| | | |||||||| |||||||||||||| || | |||| || || || ||||| || ||||| ||| |||||||||||||| | || ||||| |||||||| ||||
gtatga-ttacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgt--gaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttatt--ttgttt--------tacttctt---ccctcttggtgggcggtgta--atggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
|| ||||| | | ||| || | ||| || | || || ||||||| ||| || | || | ||| | || | ||||| ||| | || || ||| || | | || |||||||| || ||||||||| | |||| |||| || || ||||| || || || |||||||| ||||||||||||||||| |||||||| ||||| ||||
gtatgtttcacacgcacatgaactagattttatataacttg--tccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162255799|gb|FC431459.1|FC431459EST: TCACTCACGCATCACCGACCTTATTCAACGCAGGAACTCCCAGGCCACAG CTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATC
genomic: TCACTCACGCATCACCGACCTTATTCAACGCAGGAACTCCCAGGCCACAGgtaggacttg ... gggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgggcggtgtaatggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
tacttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttggtgggcggtgtaatggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA