Sequence
atgc intronic sequence ATGC exonic sequenceTTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg...
Basic information
species | Physcomitrella patens |
transcript | PP1S100_117V6.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os01g51380.1 (Oryza sativa), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccg--tggttgtgttcctagttcagaactagctcttattccttttccctg---
||||| ||||||||||| |||||||||||||| || ||||| |||||||| |||||||| || || ||||||||||| || | ||||| ||| |||||| || ||| ||| | | | ||| | | | | | | | | | | || | | || | | || | ||||
CTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAATGGAGAGAGTTACCTTATTTCTTAATCTGgtatatctgcatta-cctttgttctttcttttccttcactatgctgctctaaggaatttgcaagatctataacttactccttgattttgtattttttgttcatag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctc------acttttaatcttcatcttc-------tgtttaacacggcaaagatatcttcacc-gtggttgtgttcctagttcagaactagctct-tattccttttccctg-----------------------------------------------------------------
||||| ||||||||||| || ||||| ||||| ||||||||||||||||| || || |||||||| |||||| | || || |||||||| ||| ||||| | |||||| | ||| ||| | | | | | || || | | ||| | ||| | || || | | | | ||| | | | |
GTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacg-----gcaaagatatcttcaccgtggttgt-gttcctagttcagaactagctcttattccttttccctg
||||| ||||||||||| |||||||| |||||| ||||||||||||||||| || || || || ||||||||| | || || |||||||| ||| ||||| || || | | | | || | |||| | ||| | | || | | | ||| | | | | || | | ||
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacct-acaaggacttgtgaatttgtaaccaacattcatttatcattttatttcttctaagggcgccataatcaattctgcaatgttttacatgcatctt-----
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacg-----gcaaagatatcttcaccgtggttgt-gttcctagttcagaactagctcttattccttttccctg
||||| ||||||||||| |||||||| |||||| ||||||||||||||||| || || ||||| |||||||| | || || |||||||| ||| ||||| || || | | | | || || | |||| | | ||| | || | || | |||| | | | | || | | ||
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacct-acaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt-----
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta--tctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttat-tccttttccctg---
||||||||||||||||||||||||||||| || || ||||||||||| || |||||||| || || |||||||||||||| ||||| || ||| ||||| | | | | | || | || ||| | | || |||| || || | ||| | | || | || | | ||
-TTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGGtagtctttagaaccagtatgcaaatgctcttttattcct-----atttctttgttgtttacttgccttcatttccttctttgtaattttgtctatgtatttgaga
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttca-ccgtggttgtgttcctagttcaga-actagctcttattccttttccctg--
||||||||||||||||||||||||||||| || || ||||||||||| || ||||| || || || |||||||||||||| ||||| || ||||||||| | | ||||| | | |||| ||| | | | ||| ||| |||| | | | ||| |||| | | | |
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccc---tttaacaattaaaatctgcc-aacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatc--ttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg
||||||||||||||||||||||||||||| || || ||||| ||||| || ||||| || || || |||||||||||||| ||||| || ||||||||| || | ||| |||| | | | | | ||| || | | ||| | | || | || | | |
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaac-gtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta-
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta--tctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgt--ggttgtgttcctagttcagaactagctcttattccttttccctg---
||||||||||||||||||||||||||||| || || ||||||||||| || ||||| || || || |||||||||||||| ||||| || ||| ||||| | | | | | || | | ||| | | || |||| || ||| ||||| || || | | ||| | | |
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattccc-----atttctttgttgtttacttgccttcctgatttccttct--ttgtaattttatctatgtagtt
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtg---ttcctagttcagaactagctct-tattccttttccctg----
|||||||||||||| || ||||||||||||||| |||||||| || ||||| || ||||| || || ||||||||||| || ||||| || || ||||| | || | | || ||| || || || || | || || || ||| ||| | ||| | ||||||| |
GTTTGCAGCTATGGGTGTGAACATGGAGACAGCTCAGTTCTTCAAGCGAGATTTTGAAGAAAATGGATCAATGGAGAGAGTTACTCTTTTCCTGAACCTGgtaaat-----ttgacttctatag-ctgattgccatatcatggagttttttcaagtatttagatgtttcttagctttaaacagatttaaccttcctttattccaacag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact----tttaatcttcatcttctgtttaacacggcaaagatatcttc----accgtggttgtgttcc--tagttcagaactagctc--ttattccttttccctg-----
||||||||||||||| || ||||||||||||||| || ||||| |||||||| || ||||| || || ||||| || || || ||||| || || |||||| | ||| || | | | | || | | | || | |||| | | | || ||| ||| | | |||| | || | |
TTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGATGGAAAGGGTTACCCTTTTCCTGAACTTGgtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattatatcagtgaggaattgaccttattatgcattccactcgaacag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta--tctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg----
|| ||||| ||||| || ||||||||||| || || || ||||||||||||||||| || || || |||||||||||||| ||||| || || |||| | |||| | | | || || ||| ||| | || | ||| || || | | ||| |||| ||| ||
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactaca----------gacatcttgaagcaaattttagttccaatgtttttctg----aaggtt---tctcattctgttttccgcacag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttc-tgtttaacacggca-aagatatcttcaccgtggttgtgttcctagttcagaac---tagctcttattccttttccctg---------------
|||||||||||||||||| ||||||||||| || || || |||||||||||||||||||| || || |||||||||||||| || || || || |||||| | | || ||| || | | |||| | | | | | | || | ||||||| | ||| | | | ||| |
TTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAATGGAGAGAGTGACTCTATTCCTTAACCTGgtattt-atattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacag
upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 8
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatc--tcact--tttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttattccttt--tccctg------------------------
||||| ||||||||||| |||||||| ||||| || || || |||||||| |||||||| || ||||||||||||||||| ||||| || || |||||||| | | | |||||||| | | || ||| | | ||| || | | || || ||| | | | | || ||| ||| | ||
CTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCATGGAGAGAGTGACCCTTTTCCTAAACTTGgtatcaattaataatttaatctct-tatcctaattatgttgtttaggatgatctctc--tcatttcatt--taggtggaagggtgttttttttcttttaatatttgtaatgatgtggctcttttgcacagMapped 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|162269043|gb|FC445535.1|FC445535EST: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
EST:
gi|162221566|gb|FC397583.1|FC397583EST: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAA
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAA
EST:
gi|162278567|gb|FC454029.1|FC454029EST: TTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTNCA-TTTG GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCAC
genomic: TTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCT-CAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCAC
EST:
gi|162209307|gb|FC385227.1|FC385227EST: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
EST:
gi|162232324|gb|FC408667.1|FC408667EST: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTG GCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
genomic: ATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACT
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:
34 (upstream exon),
19 (downstream exon)
Score:
11TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcact ... tgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC
<
<
<
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA