Sequence
atgc intronic sequence ATGC exonic sequencegtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
Basic information
species | Physcomitrella patens |
transcript | PP1S267_10V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 6
gtgattcctaagcatc---tcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
|| | | ||| || ||||| | || | || || || | ||| | | || || |||| | ||| | | || | | | |||||||||||||||| |||||||| || ||||| || || |||||||||||| | || |||||||| || || || ||||||||||||||||| |||||||
gtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttat-atataacctgataagaactttggcttttgttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAACCTTTCCGCACCTCAAACATTCCGATCCAAGGAGATCTCCAAGAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 6
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
| || | | | || | ||| || | |||| || ||| || || | |||| || || | |||| ||||| || || || | ||||||||| || | || |||||||| ||||||||| |||| || || ||||| || || ||||||||||||||||| ||| |
-----------gtatatatgtacatatgatgaac---tccaactcgggt--gatcgcgatcgatga---aacatgaattggtttgttgtgcatatggaaattggcaatggcagCCGACGTCGATCGCGAGCTACAACCACCTAGGCAACAACGACGGCATGAACCTGTCGGCGCCGCAGACGTTCCGGTCCAAGGAGATCTCCAAGAGCGGCG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
||| | || ||||| || | | | | | || | | || | | | || | | || || |||| || | ||| | |||| |||||||||||| ||||||||||| || |||||||||||||||||||||||| |||| || ||||| || || | ||||||||||||||||| ||||| |
gtgggaacctagtatctctctt---ctattaagatgaagtgtttttttggcaaatg------acg--ttattgcaataactc---ttctatattttc--attttcatgca--gCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 6
gtgattcctaagcatctcgtttggttcactggaagtatccggt----tctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
|| || | | | | | | ||| || ||||| | |||| || | | | ||| || || | ||||||||||| |||||||||||||| || |||||||||||||| ||||||||| |||| || ||||| || || | ||||||||||||||||| ||||| |
------------------gtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcag------acgacata-cttacaat-aattcgtgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 2
gtgattcctaagcatctcgtttggttcactggaagtatccggt----tctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
|| || | | | | | | ||| || ||||| | ||| || | | | | ||| | | || ||||||||||| |||||||||||||| || |||||||||||| | ||||||||| |||| || ||||| || || | ||||||||||||||||| ||||| |
------------------gtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcag------acgtcata-cttacaataattcttgtatatgtt-catgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACAACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
gtgattcctaagcatctcgtttggttcactggaagt-atccggttctctttaaatcgttttctatggtttgtcac-gatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
|| ||| | || ||| | || | | || | | || | | || | || || || | ||| ||||||||||| |||||||||||||| || |||||||||||||| | ||||||| |||| || ||||| || || | ||||||||||||||||| ||||| |
--------------cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcatt-catgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G071174_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgt----tttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
| ||| | | ||||| | ||| ||| ||||||||| | || || | ||| ||| || || | || || | || || | ||||||||||||||| |||||||| ||| ||||||||||||| |||||||| | || || || || ||| || ||||| ||||||||||| |||| |
gtacgtaccatcgtcatatatgtatatctctatatataatgctgggattaattaagataatttgtgtttgacattcaagaataatctatccatctttaaatattggaattattaaagattggcacattggataataaggtggattt----gttttttcccgtagCCCACCTCAATTGCAAGCTACAACCATCTGGGAAACAACGACGGCATGAATCTCTCTGCCCCACAAGTCTTCCGGTCCAAAGAGATCTCCAAGAGCAGCG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------gtgattcctaagcatc--tcgtttggttca-ctggaagtatc-cggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
| | | || ||| | || || || | || || || ||| ||| ||| | | | | | |||| | | | ||| | || |||||| || || || ||||| ||||| |||||||||||||| ||||||||||| | ||||| ||||| ||||| || || ||||| || ||||| |||||||
gtacaacttttgttgttttgcttactaatactattgctatatcacgtgtgctactacttttattggttaataataaggacagagtatcatttgtatgcttaaactttaattaaaataaaataaaataatgtgttggctaaaaatggagaagtaaattgatgttttaattgtcttggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATTTGGGAAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCGAAGGAAATTTCCAAGAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 3
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
| | || || || | | || | || || | | || || || || |||| | | | |||| | || |||||| || || || ||||| ||||| ||| |||| ||||| ||||||||||| | ||||| ||||| ||||| || || ||||| |||||||| |||||||
----------gattttttgtatgcttaaacttta--attaaaataaaattgaagaacgtgttggggagaagtacattg-atgatgttttaattgtctgggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATCTGGGCAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCTAAGGAAATCTCCAAGAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgattcctaagcatctcgtttggttcactggaagtatccggtt-ctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
||||| || ||| | ||||| ||| |||||| | | |||||||| | | ||| | || || |||| | |||| || |||||||||||||||||||| ||||||||||||||||| ||||| | ||||| || ||||| || | || ||||||||||||||||||||||
------------------gtttgtttaacttgc-gtatcaagttactctttcttgttactgaaaatatttgtcacaagactttggtttcattgattgtgtgtttttgtttatagCCTACTTCAATTGTGAGCTACAATCACTTGGGAAACAACGATGGAATGAATCTCTCAGCTCCACAGACTTTCAGATCTAAGGAGATCTCCAAAAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaatt-attgtgca-cagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
| || || | |||| || ||| ||| | | || | | || |||| ||| || ||||| || || ||||||||||| |||||||||||||||||||| || |||||| | ||||| || ||||| || || || |||||||| || || |||||||
----------------------------gtaatagaattaaagcttgtttatcaagtaaccta--acttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtt-tgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
|| | | |||||||| | | || | |||| |||||| || || | | || || | || | || | |||| || || ||||| || ||||| ||| | || |||||||| ||||||||||||||||||||||| || || || || |||||||| || || |||||||
----------------gtacttaatcctaaataagtatcctaat----taaatttattttatatggtaacgttacaaaacgaaattaattgcattt----atctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 6
----gtgattcctaagcatctcgtttggttca-ctggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
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gtatatcattttta-gcatttcctctgttgaaatttagaattttaaagtaaataagtatgcatgtataggattatgtatgaataatgatattgaaagatgatga-tggtggtg-acagCCAACATCCATTGTGAGCTATAACCATCTGGGAAACAACGATGGCATGAATCTGTCTGCTCCTCAAACCTTCCGCTCCAAGGAGATCTCCAAGAGCAATGMapped 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|162165785|gb|FC340914.1|FC340914EST: GCAGGCATTAAG CCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
genomic: GCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
EST:
gi|162172373|gb|FC348314.1|FC348314EST: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAG CCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
EST:
gi|162150742|gb|FC327014.1|FC327014EST: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAG CCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
EST:
gi|7047392|gb|AW477286.1|AW477286EST: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAG CCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
EST:
gi|162241553|gb|FC418614.1|FC418614EST: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAG CCCACCCTCA-TTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAA
genomic: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACC-TCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAA
EST:
gi|162221112|gb|FC397753.1|FC397753EST: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAG CCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAAC
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:
33 (upstream exon),
35 (downstream exon)
Score:
20TGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattccta ... ttgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
tgaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA