Sequence
atgc intronic sequence ATGC exonic sequencegtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
Basic information
species | Physcomitrella patens |
transcript | PP1S57_70V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g22380.1 (Oryza sativa), 3'ss of exon 5
gtacaaattttggtgaatctccttttagtttgtgacaacca--cagtcgtttattgatctgcga-attttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
| | || | | ||| | ||| | || | |||| | | | | | || || | || | | | || ||||| | ||||||| || || ||||||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| ||||| | |||||||| ||||| |
-----------------------------gtattactatctgctagttagctcttgctttgtgttatttacatatgaaaatgatgaatcctgatt--gcatgcccatttctttgct--gaagGGTGCTTCGAAAAATTTGAATCTTATGGAGTGGGATAAACTCTGGACAATCAACAAGAAAATAATTGACCCAGTTTGTGCAAGGCATACTGCTGTGTTGA
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g16520.1 (Oryza sativa), 3'ss of exon 5
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagc------tttctcgattgtttgcatggca-gGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
|| | | | | ||| | | || || || |||| ||| | | | || || | || ||| | || |||||| || || ||| | ||||| ||||||||||| || ||||||||||| ||||||||||| ||||| || | ||| |||||||| || |||||
-------------------------------gtaatgttc-taatgagttaccg-tttgtgatttcatagctatatttaatggtgtcttcgtaattcatttgttctttgaccttttatttctcaagGGTGCCTCTAAAAATCTAAATCTTATGGAGTGGGATAAACTCTGGACAATCAACAAGAAGATAATTGATCCAGTGTGTGGAAGGCATACTGCCGTTCTGA
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G057491_T01 (Zea mays), 3'ss of exon 5
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaac-gattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
||||| | | | ||| |||| || ||| | | | | ||| | | | | | |||| | ||| | | | || || ||| | | ||||||| ||||| ||| ||||||| ||||||||||| || ||||||||||| ||||||||||| ||||| || | || | |||||||| ||||| ||
gtacacctctgtgctaatatcctcttgctttatctt---tatatttttttgaatgtttaatattgattgtgtatccatgtttgatcttttgaaattatagctattttttttttgttgaagGGTGCTTCAAAAAATCTGAATCTCATGGAGTGGGATAAACTCTGGACAATCAACAAGAAGATAATTGATCCATTGTGCGCAAGGCATACTGCTGTGCTAA
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G046932_T01 (Zea mays), 3'ss of exon 5
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattt---tctactatcagtaacgattctcaagc-----aagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
||||| ||| | ||| | || || ||| | | || || || || || || | | || | ||| | | || || | | || || | | ||||||| ||||| ||| ||||||| ||||| ||||| || ||||||||||| ||||||||||| ||||| || | || | |||||||| ||||| ||
gtacacctttgtgctaatgtgctcttgctttaccttcatatttcctgattgtttattcctgatttcatatccatatttcatacccattttttattttttgaaactatatatttttttgttgttgaagGGTGCTTCAAAAAATCTGAATCTCATGGAATGGGATAAACTCTGGACAATCAACAAGAAGATAATTGATCCAGTGTGCGCAAGGCATACTGCTGTGCTAA
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G22170.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------gtacaaattttggtgaatctccttttagtttgtgac-aaccacagtcgtttattgatctgcgaatt--ttctactatcagtaacgattctcaagcaagct--ttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
|||||||| ||| ||| |||| | | | | | | || || || | || ||| ||| | | | || |||||| | | | | ||| | | |||||| || || || ||| | ||||| ||||| ||||||||||||||||| || || |||||||||||||||||| | ||||| || || || ||||| ||
gtatgttaaaggttttggtttcatttatttttaaaaaaggaaaaagaaagatgcatcattctctatttctctaacaaattt----gaaatgataagtagaatgtgtttagcaatggatatgtttttatttgtgttttcattcctgtattactcat-atgctcaagaatgttgatgactctttgatactcttgcagGGGGCGTCCAAAAATCTCAATCTCATGGAATGGGACAAGCTCTGGACCATTAATAAGAAGATTATTGACCCTGTCTGTCCTAGACACACTGCTGTCATTG
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G28180.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------gtacaaattttggtgaatctccttt------tagtttgtgac-aaccacagtcgtttattgatctgcgaattttc-tactatcagtaacgattctcaagc----aagctttctcgattgtt------tgcatg-gcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
| || | | ||| | | ||| |||| | | | || | | || || | |||||| | | | ||| | || | || | || || | || | | | ||||| || || || ||| | ||||| ||||| ||||||||||||||||| || || |||||||||||||||||| | ||||| || || || ||||| ||
gtatgcaaaaggttttgcttttgtttattaaaaaaatggaaaaagaaagatgcattctctaacaaatttgaaatgacaagtagaatgtgtttagcaattgttatgtttttattattgtattttcattcctgtattaattactcatatgctgaagaatgttgatgactcttctctgatactcgtacagGGGGCGTCCAAAAATCTCAATCTCATGGAATGGGACAAGCTCTGGACCATTAATAAGAAGATTATTGACCCTGTCTGTCCTAGACACACTGCTGTCATTG
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv14s0060g00110.t01 (Vitis vinifera), 3'ss of exon 4
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
| || || | || ||||| |||||| | | ||| || | || || | | | | | || |||| || || || |||| | ||||| ||||| || ||| | ||||| ||||| ||||| || |||||||| || || |||||||||||||| ||| | |||||||| ||||| |||||| ||
atgcatccttaaatccatgctattttatgttgtgaaagtc-------tttgttattttggccatcct--------aatgaaggttaatgagca---ttcttctatcctttg-gtttcagGGGGCATCGAAAAATCTCAATCTCATGGAATGGGATAAACTCTGGACCATTAATAAGAAGATTATTGATCCTGTCTGTCCCAGACATACTGCTGTTATTG
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDO97532 (Chlamydomonas reinhardtii), 3'ss of exon 6
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagta-acgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT---------------------------
| ||| | |||| | | ||| || | ||| | |||| | | || || ||| | | ||| || | | | | ||||||||||||| ||||||| || ||||||||| | |||||||| | || || | || || || ||
--------------------------------------------ccctttgcaggtctgggcgtggcctaatagaatcccacgtgtttcaaatcactgaacccgctt-cctgcgccccctg-cgca-cacacccgccgccaccgcagGAGTGGGACAAGATCTGGACCATCAACAAGAAGCTGATTGACCCGGTGTGCCCTCGCCACACGGCCGTGGACGTGGAGGGCAAGGTGCTGCTGACGCTGG
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ12718 (Selaginella moellendorffii), 3'ss of exon 4
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
| | || | ||| | | || || | || | | | | |||| | | ||||| || ||||||||| |||| |||||||||||||||||||| ||||| || |||||| ||||||| ||||| |||| || ||||| || || || |
------------------------------------------------------gtaagaaaaatctctgggaac--tattgagtttctaacga---tcctcgtgttcctttcctccagGGCGCGTCAAAGAATCTGAACCTGATGGAGTGGGACAAGCTATGGACGATCAACAAGCAGATTATCGACCCGGTTTGCCCGAGGCACACGGCGGTCTTGA
upper sequence: PP1S57_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ13872 (Selaginella moellendorffii), 3'ss of exon 4
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
| || | ||| | | || || | |||| | | |||| | | ||||| || ||||||||| | || |||||||||||||||||||| ||||| || |||||| ||||||| ||||| |||| || ||||| || || || |
-----------------------------------------------------gtatgaaaaaatctctgggaac--tattgagtttcaaatga---tcctcgtgttccttttctccagGGCGCGTCAAAGAATCTAAACCTGATGGAGTGGGACAAGCTATGGACGATCAACAAGCAGATTATCGACCCGGTTTGCCCGAGGCACACGGCGGTCTTGAMapped 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|162262308|gb|FC437635.1|FC437635EST: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAG GGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATA
genomic: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAGgtacaaattt ... tgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATA
EST:
gi|162158739|gb|FC335080.1|FC335080EST: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAG GGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATA
genomic: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAGgtacaaattt ... tgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATA
EST:
gi|162168564|gb|FC344475.1|FC344475EST: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAG GGTGCATCAAAGAATTTGAATCTGATGGAGTGGGANCA-GCTCTGGACAAT
genomic: TTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAGgtacaaattt ... tgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGA-CAAGCTCTGGACAAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
11 (upstream exon),
35 (downstream exon)
Score:
3ACGAGTGGAGGGTTGGAACGATCCTCGTTTTCCGACAGTTCAAGGCATTATTCGTAGGGGTCTCACAATTGAGGCTCTCAAGCAGTTTATCTTATCTCAGgtacaaattt ... tgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
cagtaac putative branch site (score: 3)
attgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaattttggtgaatctccttttagtttgtgacaaccacagtcgtttattgatctgcgaattttctactatcagtaacgattctcaagcaagctttctcgattgtttgcatggcagGGTGCATCAAAGAATTTGAATCTGATGGAGTGGGACAAGCTCTGGACAATAAACAAGAAGATTATTGACCCTATTTGTCCCAGGCATACAGCTGTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT