Sequence
atgc intronic sequence ATGC exonic sequencegtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtatgcta-aatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | | ||||||||||| |||||| ||| | | |||||| || || | | ||| || | | || ||| || || | | |||||||| ||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||| || || |||||||||||||| || ||||||
gtaagttttgatctgaaattattatctt-actacct-gtagttggtt-aacatcctcaccttaaa----aagattatg---aactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
----gtatgctaaatctgaaattactatctttacttcttcatagttgatt--caataccatcaactca-tattacaaaattctggtcaatttctct-tagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| || || | || ||| | ||||||| || || ||| | | | | | | ||| | || | | ||| ||| | || || || |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||||||| | || || || |||
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------------------------------------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtca-atttctctt-------agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | | | | | | | | | | ||| ||| | | | | || | | | | || | ||| ||||| || || | |||||||||||||||||||| ||||||||||| || || ||||||||||||||||| || ||||| || |||||||| || || || || ||
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
-----gtatgctaaatct-gaaattactat----ctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | | | ||| || | | |||| | || | || ||| | | || | ||||| || | | || | | | || ||| | ||||| || ||||||||||| || |||||||| || |||||||||||||||||||| |||||||| || ||||||||| | || || || |||
ctgaactattttttgtttcaaaactattgtaattctttgttgttttactatt-atttactccctgatatatatattctttcatatttgaaaaactat-tcagTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20590.1 (Glycine max), 3'ss of exon 9
------------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| | | | || | ||| || | |||| | |||| |||| | | |||| | | | ||| | | | | || || | |||||||||||||||||||||||||||||||| || |||||||||||||| || || || ||||| || |||||||| || || || || ||
ttaagttgttaggtgatgtcatttaaaaggttttat-ttcatctcttaacagttc-ctcaagatgaa-aactaaattcatctcattgacat-gttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGATGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactca-tattacaaaattctggtca-attt-------ctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| |||| | | | | | || | ||| | |||| || | || || ||| | || | | || ||| |||| | || ||| | || || || |||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| || ||||||||| | || || || |||
ctgaactaattattgtttcaaaactattg-taattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
--------gtatgctaaatctgaaattactat-ctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| || | | | | ||| | |||| ||| | | | || |||| || || ||| || | | | || ||| | ||||||||||||||||||||||| ||||| || || || ||||||||||||||||| || ||||| || |||||||| || | || || ||
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatct-tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01210.1 (Glycine max), 3'ss of exon 10
----------gtatgctaa-atctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| | || | ||| | || | |||| | | || | || | | | ||| | | ||| | | | | || || | |||||||||||||||||||||||||||||||| || |||||||| ||||| || || || ||||| || |||||||| || || || || ||
ttaagtggttaggtgatggcatgtaaaaggtttcatttcagctcttaacaattc-cttaaaatgaaaactgcat-tcatctcattgacat-gttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGACGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
---gtatgctaaat-ctgaaattactatct-ttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| |||| | ||| || | |||| | || || | | | | ||| | || | || ||||| ||||||| | || || ||||| |||||||| || |||||| | || ||||||||||| || || ||||| ||||| ||||| ||||| ||||||||| |||||
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaat---gttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | | || | || | | | ||| |||| | || || ||| || ||| | | |||| | | || | | |||||| | ||||| || ||||||||||||||||||||||| || |||||||||||||| ||||| || || || ||||||||||| || ||||| || |||
atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttt--tttaattttat-gtctctgttctcctaattattattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactc--atattacaaaattctggtc-----aatttctctt-----agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | ||| || || || || |||| || | | | | || | || ||| ||| || || |||| | || || | ||||| |||||||||||||||||||||||||| || || |||||||||||||| || ||||| || ||||||||||| || ||||| || ||
-tatattttgcctgtggacggtagtttctttttctc---gttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
--gtatgctaaatctgaaattactatcttt-acttcttcatagttgattcaataccatcaactcat-attacaaaatt--ctggtcaatttctctt--agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | || | | |||| ||| | | | | | || | || | | | | ||| | | | ||| | |||||| | |||||| | || |||||||| |||||||| || ||||| || || ||||||||||||||||| ||||| || || ||||| ||||| || | || |||||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaatt--ctggtcaatt---tctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | || | | || || |||||| | | | | ||| | || | || ||| | | | | | | |||||| | || ||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| || || || || ||||| |||||| | |||||||
accagta-gttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------gtatgctaaatctgaaattactatctt-tacttct-----tcatagttgattcaatacc-atcaactcata-ttacaaaattctg-gtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | ||| || | | | | |||| || |||| | | || | | | | || || || || || ||| | || | || ||| | || ||| | || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||| || || ||||||||||||||||| |||||||||
gtaggaactgcttttgtcatggtttttcagcacggagattaactc-gtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaata---cgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATGMapped 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|211520168|gb|FL238542.1|FL238542EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATTTTGCTCCTGAATATGCAATGACTGGCCATC
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATC
EST:
gi|101397928|gb|EB820841.1|EB820841EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST:
gi|211132438|gb|FL443442.1|FL443442EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST:
gi|211541315|gb|FL466512.1|FL466512EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST:
gi|5268951|gb|AI770915.1|AI770915EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST:
gi|211541314|gb|FL466511.1|FL466511EST: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
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 4 RNA-Seq libraries.
Block sizes:
40 (upstream exon),
47 (downstream exon)
Score:
81AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
Block sizes:
48 (upstream exon),
46 (downstream exon)
Score:
59AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
Block sizes:
45 (upstream exon),
46 (downstream exon)
Score:
110AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
44AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
agttgat putative branch site (score: 44)
tttctctt putative PPT
tcatattacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA