Sequence
atgc intronic sequence ATGC exonic sequencegtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------gtcagtaatcatttttttaccacttgatgac--tcgatctcttgat--atgcaaatctttttgacaagtgatcattctggctgcg--------cagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|||| | ||| | || | | | | || || ||| || || || | ||| || | ||||| | ||||| ||||| || ||||| ||||| |||||||| ||||||||||||||||| || || || || || ||||| ||||| ||
gttagtagctagcaaatgtgccaacaatcattagaaacttcttcagaattcacctgttattccttgtgtcattatctatttctcaatgcattcagaattttcgtttccatgttttgactggcagttaatgatttcagGCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
---------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgat--cattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| | | | |||| || | ||| |||| | | | |||| | | | ||||| | | | | || ||||||| || || || ||||||||||| ||||| || || || |||||||||||||||||||| || || ||||||||||| ||
acatttggtaacctcttgtctgactttgttttgacaagttgctgacccc-tgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattct----ggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| || || ||| || || |||| || ||| || || | | || |||| |||||| || || || || |||||||| || || || |||||||||||||||||||||||||| || || |||||||||| ||
ttttgcctcagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
--------------gtcagtaatcatttttttaccacttgatgactcgatctc--ttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| ||| || | || || | | ||| | | || | ||| | | ||| | ||||||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| ||
ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 6
------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattct----ggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| || || ||| || | | |||| || ||| || || | | || |||| |||||| || || || || |||||||| || || || |||||||||||||||||||||||||| || || |||||||||| ||
ttttgcctcagttttgacaagttttctttccccttctcgccatacgataactatatagattgatggcattttaagcttttctttctttgcaataatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
----------------gtcagtaatcatttt-tttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|| || || | |||| | | |||| |||| | | | | || | | ||| | | ||||||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| ||
ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttt-tgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 5
---------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtga---tcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|| | | | |||| | | ||| |||| | | | |||| | | | ||||| | || || |||||| || || || ||||||||||| ||||| || || || |||||||||||||||||||| || || ||||||||||| ||
atttggtaacctcttgttc-tgactttgttttggcaagttgctgacccc-tgttttgacaaactacgacatttgaagcttttctttcttttcaatactgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G03920.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtaatcatttttttaccacttgat----gactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcg--------cagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|| ||| | || | || || ||| | | || | || | || || | | | || || | | | | || ||||||||||| ||||| || |||||||||||||| || || ||||| | | |||||||| ||||| ||||||||||||||
gtatgtactt-cttatctatcaaaagatctctaatttgaaatatttctttgattatgtgtctaacttgtagttggtgttggtgtatcacttaacagGCTTACTCAACCGTTGGTACACCAGACTACATTGCACCTGAAGTCTTGTTAAAGAAAGGATACGGCATGGAATGTGACTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------gtcagtaatcatttttttac-cacttgatg--actcgatctc-ttgatatgcaaatctttttgacaagt---gatcattctg------gctgc-----gcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| | |||||| |||| || | ||| | | |||| |||||| || | || | ||| | | | ||| | ||| ||||||||| || || || ||||| || ||||| || |||||||||||| | |||||||||| || || ||||||||||| ||
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 5
------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| || ||| ||| | || |||| | || ||| || ||| || ||| |||||||| || || || || |||||||| ||||| |||||||||||||| ||||||||||||| |||||||| ||||||||
gtaaggcttcatattcacctttgagattttcaatagagtt-tctccctctgtgtgtgtctgattaacacatg-tcacg--------acagGCTTATTCCACAGTTGGCACACCAGATTACATAGCTCCAGAAGTTCTGTTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtcagtaatcatttttttaccacttgatgactcgatctcttgata-tgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|| | | || ||| | | || | | | | | | ||| | || |||| ||| |||||| || || || || || || || |||||||| ||||||||||| || || |||||||| || |||||||| ||||| ||
tcactttgtttcctctgttataagaaatgtttatgcaggaccctgcgctaactgcataagggtttatatcaactaaacttttgat-attggaatactgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
--------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaa-------atctttttgacaagtgatcat-tctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
||| | | ||| | | | | |||| || || ||||| | || |||| | | ||||||||| || || || || ||||||||||| ||||||||||||||| | |||||||||| || |||||||||||||| ||
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------------------------gtcagtaatcatttt---tttaccacttgatgactcgatctcttga----tatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| | || |||| | || || || | | || | | || || |||| | | | | | | ||| ||||| || || || ||||| || ||||||||||||||||| ||||| || ||||||| || || |||||||| ||||||||
gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctgcgcgcgagaattcacgcgcgtacattctttttagatatatgacctgtggtttttatttttcgaccactagtcaaacatcaagtattaattccaggttttgctcatcagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------gtcagtaat--catttt-----tttaccacttgatgactcgatctcttgatatgcaaatctttttga----caagtgatcattctg-gctgcgca----gGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
|||| || ||| || ||| | || || | | | | ||| | | | ||||| | | | | | |||| ||| || || || ||||| || ||||| || || ||||| ||||| || |||||||||||||| |||||||| ||||||||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gtcagtaatcatttttttaccacttgatgactcg-atctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| | || | | || | | | | || ||| | ||||| || || |||||||| || || ||||| || ||||| || || ||||| |||||||| |||||||| || ||||||||||| ||||| ||
----------------------gtgcgtagcttgtacttccttttgtcccgatttttatc-taagtgttcttta-------acagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gtcagtaatcatttttttaccacttgatgactcg-atctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
| | || | | || | | | | || ||| | |||| | || |||||||| || || ||||| || ||||| || || ||||| |||||||| |||||||| || ||||||||||| ||||| ||
----------------------gtgcgtagcttgtacttccttttgtcccgatttttatc-taagtttccttta-------acagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTGMapped 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|71298682|gb|DR785316.1|DR785316EST: GCTCGCAGCAAGAACAGCTGGAGCACTGGCAGAAGAACAGAAGAACCCTG GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTG
genomic: GCTCGCAGCAAGAACAGCTGGAGCACTGGCAGAAGAACAGAAGAACCCTGgtcagtaatc ... ggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTG
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:
10 (upstream exon),
40 (downstream exon)
Score:
1GAAGTCGTCGGCGATGCATGGGGACGGGAAGCAGCAGTCGATGCCGAAGCGCTCGCAGCAAGAACAGCTGGAGCACTGGCAGAAGAACAGAAGAACCCTGgtcagtaatc ... ggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
ttttgac putative branch site (score: 1)
aaatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA