Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
Basic information
| species | Selaginella moellendorffii |
| transcript | EFJ21576 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------gtaagttcgtttattcgtagtgt------ctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| || ||||| | | ||| | || | |||||||||| |||||||| || || | || ||||| |||||||| |||||||| || ||||||||||| || ||| |||| || ||||||
gtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagTTTATGCAGATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATGATGTTGCTGCGATATTGACCTCTATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G120674_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| | | ||| | | | || | | | | |||| ||||| ||||||||||| ||| | |||||||| ||||| ||||||||||| || ||||||||||| |||||| |||| || || |||
gtatgttctctttagatgttaaggaactaaattatcctcatgtattgacacctgaatagatttacaataagtggtttaataccattttttt-cagTCTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGCCCTATATATGATGTTGCGGCAATATTGACCTCTATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| ||| | || | |||| | | || | | |||||||||| ||||||||||| ||| | |||||||| ||||| |||||||| || || || |||||||| |||||| |||| || || |||
gtatgttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
-------------------gtaagttcgtttattcg-tagtgtctatcttccttacgcgctctc-----gcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
|| ||| | | | | | | || ||| || | ||||||||||| ||||||||||| || | || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || ||||||
tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 2
----------------------------------------------gtaagttcgtttattcg-tagtgtctatcttccttacgcgctctc-----gcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
|| ||| | | | | | | || ||| || | ||||||||||| ||||||||||| || | || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || ||||||
ctcctctggcttattctgatacaactctcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G074479_T04 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------gtaagttcgtttattcgtagtgtc-tatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
|| || | || | | || | | || | ||||| ||||| ||||||||||| ||| | || ||||| || || |||||||| || || ||||||||||| ||||| | || || ||||||
gtaatatttctttccttccccacattttttgctgacctcatcaccctctgtctttgtgcacattaacatcaatctcaattttgattttgtagaaagtggtgtaacattttattattaatgcagtatatgctgatggaagcatctgtttggatatcctacagAACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G02400.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcg----cagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
||||||| | ||| | ||| ||| |||| | | || ||||||||| ||||||||||| ||| | ||||| | |||||||| ||||||||||| ||||||||||| || ||||| || || || |||
gattaatgaatctgtatggaaataagtaattaagtactatttgcttttgtcaagttcggtaatttgcagt-tctgagccccttttcctttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G02400.2 (Glycine max), 3'ss of exon 4
-------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcg----cagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG-----------
||||||| | ||| | ||| ||| |||| | | || ||||||||| ||||||||||| ||| | ||||| | |||||||| ||||||||||| ||||||||||| || ||||| || || || |||
gattaatgaatctgtatggaaataagtaattaagtactatttgcttttgtcaagttcggtaatttgcagt-tctgagccccttttcctttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGGTCATAGTGAT
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctc--tcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
|||| | | | | ||| | | | || | || | ||||||||| ||||||||||| ||| | ||||| | |||||||| ||||| ||||| ||||||||||| |||||||| || || || |||
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 4
----------------------------------gtaagttcgtttattcgtagtg-tcta--tcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| | | |||| || | |||| || | || | || | ||||||||| |||||||| |||||| | || || || |||||||||||||| || || |||||||| || || ||||| ||||| ||||||
gtaagtattaggtggaaaatctttacgttggagtatcaataaatttagctgtgtagctctaattcattttttcaacttcgtgtagTTTATGCTGATGGAAGTATTTGTTTGGATATACTACAAAATCAGTGGAGTCCTATATATGATGTGGCTGCTATACTCACATCTATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G20310.1 (Glycine max), 3'ss of exon 3
---------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
||| || | | | | | | || | | | ||||||||| |||||||| |||||| | || || | |||||||||||||| || || |||||||| || || ||||| ||||| ||||||
gtaagtattgggtggaaattggaaaatctttaccttggagtatcaataaattagctgtgtagctctaattcattttttcaactttgtgtgtagTTTATGCTGATGGAAGTATTTGTTTGGATATATTACAAAATCAGTGGAGTCCTATTTATGATGTGGCTGCTATACTCACATCTATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G62540.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------gtaagttcgtttattcgtagtgtctatcttccttac-gcgctct--cgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
|||| | ||| | | || | || | | | || | ||||||||||| |||||||||||||| | || ||| | ||||| ||||||||||| ||||| || ||||| ||| | || ||||| || |||
gtaagcccaagcattcagtgaacaacatagtaa-tagaccaattaggaaattcgactttgataattgaactttggtgcagTTTATGCTGATGGAAGCATTTGCTTGGATATCTTGCAAAACCAGTGGAGCCCCATCTACGACGTTGCTGCAGTTCTCACATCAATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
||| | | | | | |||| ||| | | | |||||||||| |||||||||||||| | ||||| || |||||||||||||| || || |||||||| || || ||||| ||||| ||||||
catgatgatgatcatcataatgtttttagcttttttgaggaaactaaactaagtattattttgctgttgctggctctaagttctcttaatcttttgtcagTTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcg-------cagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| || |||| | || ||| |||| | | | |||| ||||| |||||||| ||||||||||| || || |||||||||||||| || || |||||||| || || ||||| || || || |||
gtaagttggaactatgttgcaattagtatcacttcatgttaaatatttctttagctgcggtttcttacttctaccttttattttgaattggccagTCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
-----------------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgc-----gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| | | | | | | | | | ||| | | | ||||| ||||| || || |||||||| || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || ||||||
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
upper sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------gtaagttcgtttattcgtagtgtctat-cttccttacgcgct-ctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
| | || | | |||| ||| | | | | |||| ||||| || || ||||| || | || ||||| ||||||||||||||||||||||| || || || || || |||| ||||| |||
ctagcgcttgtgttgaggacgtttggagtccctgggcgtggagccgagagggacacagcgcgcgtctct-gtgtttatgcggtggtgtttgtggcaaacagTATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAGMapped 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: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACA TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
genomic: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACAgtaagttcgt ... gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
EST:
gi|169054452|gb|FE460274.1|FE460274EST: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACA TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
genomic: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACAgtaagttcgt ... gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
EST:
gi|169060609|gb|FE467347.1|FE467347EST: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACA TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
genomic: CAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACAgtaagttcgt ... gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCC
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:
35 (upstream exon),
26 (downstream exon)
Score:
58GTACGTTCAAGCTTACGTTACAGTTCACGGAGGACTATCCCAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACAgtaagttcgt ... gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
tccttac putative branch site (score: 58)
cgctctc CT-rich tract
tttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcgtttattcgtagtgtctatcttccttacgcgctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
