Sequence
atgc intronic sequence ATGC exonic sequenceTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag
Basic information
| species | Selaginella moellendorffii |
| transcript | EFJ21576 |
| intron # | 4 |
| splice site | 5' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttgcttgcaagt--gttgagc-tgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------------
||||||| |||||||| || || | || ||||| |||||||| |||||||| || ||||||||||| || ||| |||| || |||||||| | ||| | | | ||| | | |||| | || | | ||| || ||| ||| | |
TTTATGCAGATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATGATGTTGCTGCGATATTGACCTCTATCCAGgtatcatttgaaccttcgcagagtgtcctaacaatcacatcgatagcttcacttggtttaatgctttcccctggttgtagctcacttgattacaatcatt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os03g57790.2 (Oryza sativa), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttgcttgcaagt--gttgagc-tgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------------
||||||| || || | || ||||| |||||||| |||||||| || ||||||||||| || ||| |||| || |||||||| | ||| | | | ||| | | |||| | || | | ||| || ||| ||| | |
---------ATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATGATGTTGCTGCGATATTGACCTCTATCCAGgtatcatttgaaccttcgcagagtgtcctaacaatcacatcgatagcttcacttggtttaatgctttcccctggttgtagctcacttgattacaatcatt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttct--tcttgttcttccag-----------------------------
| ||||| ||||||||||| ||| | |||||||| ||||| ||||||||||| || ||||||||||| |||||| |||| || || ||||| | | ||| | | | || | || ||| ||| ||||| || || |
TCTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGCCCTATATATGATGTTGCGGCAATATTGACCTCTATTCAGgtatcactcattttgtcactcaacctatcatg-ttgaaataacttcgttttgttctaacactgcctgtctattatactgctctaatggattattgtatcca
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G007260_T02 (Zea mays), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttc--ttcttgttcttccag--------------------------------------------------------------------------------------------------------------
||||||| ||||||||||| ||| | |||||||| ||||| |||||||| || || || |||||||| |||||| |||| || || ||||| ||||| | ||| | | | || | || | ||| |||| | || || |
TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctcatatttgtcactcaacctatcatg-ttgaaataaccccattttgttcgatcactgcctgtctattgtattgctgtaatggattattgtatttgtatccagtagaaagctgaaagctcatgcatttggtcccacctaactgaattggcattgttataatttcaattgccatatag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttc--ttcttgttcttccag----------------------------
||||||| ||||||||||| ||| | |||||||| ||||| |||||||| || || || |||||||| |||||| |||| || || ||||| ||||| | ||| | | | || | || | ||| |||| | || || |
TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctcatatttgtcactcaacctatcatg-ttgaaataaccccattttgttcgatcactgcctgtctattgtattgctgtaatggattattgtattt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 3
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag-------------------------------
||||||| ||||||||||| || | || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || |||||||| | | | || | || || | || || |||| |||| | |
TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccatacaaga-aatcttttatttcttacaagagattattgtttttccaacatttgtaacttttgcttgttatacagtaacattcaactttgcagt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA01G05080.1 (Glycine max), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------------------
||||||| ||||||||||| ||| | ||||| | |||||||| ||||| ||||| ||||||||||| |||||||| || || || ||||| | | | | | | || || | | | || | | | | | || |
TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtca--cagtgattctctatattttggcattgctttaagactattaatgttaacactaatttgattgtatcccatcccaaaatctgtgtacctttcttttga
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA02G02400.1 (Glycine max), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------------------
||||||| ||||||||||| ||| | ||||| | |||||||| ||||||||||| ||||||||||| || ||||| || || || ||||| | | | | | | | | || || | | || | | | | | || |
TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtca--tagtgattctctatattttggtattgccttaagactattaatgtgaacactaatttgattgtatcccatcccaaaatctgtgtacctttcttttga
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-------------ttgcttgcaagtgtt------gagctgcgaacactga------------ctccaagtttttcttttcgttcttcttgttcttccag
||||||| |||||||| |||||| | || || || |||||||||||||| || || |||||||| || || ||||| ||||| |||||||| || ||| | | || || || | | | || | || | | || | | ||| | ||||| ||
TTTATGCTGATGGAAGTATTTGTTTGGATATACTACAAAATCAGTGGAGTCCTATATATGATGTGGCTGCTATACTCACATCTATCCAGgtatcatctagtattttatttgtatattttacaaatgaactaagcaagcagatattttgtacatcattaaatctatcactaaaattttcattttctttca-
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA06G20310.1 (Glycine max), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-------------ttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag-----------------
||||||| |||||||| |||||| | || || | |||||||||||||| || || |||||||| || || ||||| ||||| |||||||| | ||| | | || | || | | | |||| || || | | | | |
TTTATGCTGATGGAAGTATTTGTTTGGATATATTACAAAATCAGTGGAGTCCTATTTATGATGTGGCTGCTATACTCACATCTATCCAGgtatcatctagtatttcatttgtatattttacaaatgaaccaagcaagcagatatttttacatcattaaatctatccctagaatttccatttgctttcaa
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT5G62540.1 (Arabidopsis thaliana), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgttt--gcttgcaagtgttgagctgcgaacactgac----tccaagtttttcttttcgttcttcttgttcttccag-------
||||||| |||||||||||||| | || ||| | ||||| ||||||||||| ||||| || ||||| ||| | || ||||| || ||||||| ||| | | | | | | | | | | ||| | | | | | | |||
TTTATGCTGATGGAAGCATTTGCTTGGATATCTTGCAAAACCAGTGGAGCCCCATCTACGACGTTGCTGCAGTTCTCACATCAATTCAGgttttgacttctgaattcttcatttgtatcttttgcattgtggaggttatgcatgaactaaaccaagaccttttgttttacag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactga-----ctccaagtttttcttttcgttcttcttgttcttccag---------------------
||||||| ||||| || || || | ||||| || ||||| |||||||| || |||||||||||||| || ||||| || || |||||||| | || || | | || || || || || | |||||||| | | |
TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattca-aaatgccatatgaacatctcttgatgcccttaaaagcttgaattgctttcttcttctctaatccgtttttccctttgttattgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 5'ss of exon 6
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttg--------cttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag----------------------
||||||| |||||||||||||| | ||||| || |||||||||||||| || || |||||||| || || ||||| ||||| |||||||| ||| | | | |||| | || || ||| | | ||| | | | |
TTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAGgtattggatatgttcatattattgtttggatgttg-catcaactgagaacatgatatttaaaacatgaaagaatgctgatttgacctatgtttttgccttt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 5
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgt-ttgct----tgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag-------------------------
| ||||| |||||||| ||||||||||| || || |||||||||||||| || || |||||||| || || ||||| || || || ||||| ||| | ||| | || | | || || | ||| | || | | | |
TCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaatatacaattattatgtggataatgttgccattgtttttagttaacaattgtatgagggacttaactacaagaaaatgtgaccattcatat
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttg----------agctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------
| ||||| || || |||||||| || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || |||||||| | || || | | | | | | || || | || | || || |
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S91_88V6.1 (Physcomitrella patens), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgac--tccaagtttttcttttcgttc------ttcttgttcttccag----------------------
| ||||| || || ||||| || | || ||||| ||||||||||||||||||||||| || || || || || |||| ||||| ||||| | | | ||| | | |||| | |||| | |||| | | | || | ||||
TATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAGgtgagtgatcgtgatgccagcaggtgtccgtgacattgtaagtcggttgattcggttgagacgtagtggtgcgaccaggaacgtgagagtattcgaagta
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 4
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgac--tccaagtttttcttttcgttc------ttcttgttcttccag----------------------
| ||||| || || ||||| || | || ||||| ||||||||||||||||||||||| || || || || || |||| ||||| ||||| | | | ||| | | |||| | |||| | |||| | | | || | ||||
TATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAGgtgagtgatcgtgatgccagcaggtgtccgtgacattgtaagtcggttgattcggttgagacgtagtggtgcgaccaggaacgtgagaggggtgttggaaMapped 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|169060608|gb|FE467346.1|FE467346EST: ATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG TCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
genomic: ATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgc ... gttcttccagTCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
EST:
gi|169054452|gb|FE460274.1|FE460274EST: ATCAGTGGAGCCCGATTTATGATGTTGCCGCAATACTGACATCGATCCAG TCTTTGCTATGCGATCCGAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
genomic: ATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgc ... gttcttccagTCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
EST:
gi|169060609|gb|FE467347.1|FE467347EST: ATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG TCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
genomic: ATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgc ... gttcttccagTCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCG
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:
26 (upstream exon),
33 (downstream exon)
Score:
42TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgc ... gttcttccagTCTTTGCTATGCGATCCCAACCCAAACTCTCCTGCTAACTCCGAGGCGGCGCGCATGTACAACGAGAACAGGAGAGAGTATAACAAGAAAGTTCGAGCAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttgagctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag
- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - GTGGAG
