Sequence
atgc intronic sequence ATGC exonic sequence...ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57080.1 (Oryza sativa), 3'ss of exon 7
--ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
| | | | || | | | ||| | || || | || | | || | || ||| | ||||| | |||| || ||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||| ||||||||||||||
aaaccacacctttctag-gatagacaaaatgtaacttgctgctgaatttcatttaattactccctgtccc-atagaagttaatttattatttgatcgaacagGTACGTTGCTCCAGAATATGCCATGACCGGGCATCTTCTTGTGAAGAGTGATGTCTACAGTTACGGTGTTGTCTTGCTGGAGCTTTTATCAGGAAGGAAG
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
ttcgtgctatcacaataat-tgttttcctacac-tttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
|||| | ||| || ||| | | | ||| | | || ||| | || | || |||| | || || | | ||| |||||||| ||||||||||||||||| |||||| | || ||||| || ||||| || |||| ||| ||||| |||| || ||| | |||| || ||
cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctac--ctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G32640.1 (Glycine max), 3'ss of exon 8
------ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
| ||| | | | || ||| | || | || || || | |||||| | | ||| |||| | | ||||| | | ||| |||||||| ||||||||||| ||||| |||||| | ||||| || || ||||| || |||||||| ||||| |||| |||||| | |||| || |||
taagaaatggtgggactatgggaggtgcattc-tgtttttcatgcattacaaattccaggttttta----atttgatgcc-ttttctctgatctttaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTTGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 7
ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
||| ||| | || | | | | | | | |||| | | | | | | | | || || || ||||| || |||||||||||||| ||||| |||||||| ||||||||||| |||||||| || || | || || ||| || | || || |
--------------gtaaa-atttctttccaactcaaatatgatgaatacagacactctg---gacttacagtgactaccctggaaat--aatttc--agGTACGTGGCTCCTGAGTATGCAATGACGGGGCATCTCCTTGTTAAAAGCGATGTCTATAGTTATGGTGTAGTTCTACTAGAGCTTCTAACCGGTAGAAGA
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
---ttcgtgctatcacaataattgttttcctacactttgta-cacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
|| ||| | || ||||| | | |||| | || | || | |||||| | || | | ||| | ||| ||| || ||||||||||| ||||||||||||||||| ||||| ||||| || || ||||| |||||||||||||| || ||||| || ||| | || ||||| ||
catttaatgc--gtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgc--agGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
----ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
|| | || | | | | ||| | | | | | ||| || ||| || | | | || || | ||||| || || ||||| || || || |||||||| || |||||||||||||||||||| || ||||||||||| || || | || || || | || ||| ||||
ttcttttacattggaccacatctagaactaccacattaatcagaatgtcaggacttagccttggttt--ctgcactgacctattggttgattcaaactgc--agGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
-ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
|| | | | | | || || | ||| | | | | ||||| ||| || | | | | || ||| ||||| || || |||||||| ||||||||||| |||||||| |||||||| || ||||| |||||||| ||| | || |||||| | || || |||| |
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttg-tcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ20296 (Selaginella moellendorffii), 3'ss of exon 2
ttcgtgctatcacaataattgttttcctacactttg-tacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactg-cacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
||| ||||| | || ||| || | ||| ||| | | | | | | ||| || |||| | |||||| || |||||||| || |||||||| || |||||| | || ||||||||||||||||| || |||||||| | || || || | || || || |||
--------------------------gtacgctttggttttcaacagcgtagt----tttcttttatcctctgagaaactgatctctggtttactggcgcagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTCGGGCAGAAAG
upper sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ23292 (Selaginella moellendorffii), 3'ss of exon 2
ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
|| | ||| ||| | ||| | | ||| | | ||| | | || | | || ||| || |||||| || |||||||| || |||||||| || |||||| | || ||||||||||||||||| || |||||||| | || || || | || || || |||
--------------------gtaagctctggttttcaacagcgtagt-tttctcttgtcctctgag--aaactgatctctggttttct-----ggcgcagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTCGGGCAGAAAGMapped 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|22472347|gb|BU036827.1|BU036827EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
EST:
gi|26558365|gb|CA830600.1|CA830600EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAG
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAG
EST:
gi|78111224|gb|DV529621.1|DV529621EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
EST:
gi|211022043|gb|FL376172.1|FL376172EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCAATCTTCTTGTTAAGAGCG
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCA-TCTTCTTGTTAAGAGCG
EST:
gi|211382342|gb|FL400555.1|FL400555EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGC
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGC
EST:
gi|211107547|gb|FL406864.1|FL406864EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
EST:
gi|87157311|gb|DY402100.1|DY402100EST: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGG TTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
genomic: GCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGA
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:
48 (upstream exon),
49 (downstream exon)
Score:
150TAGAGGAAGATTTCACTCCTAAAGTGACCGATTTTGGTTTAGCAAGGGAAGCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
Block sizes:
40 (upstream exon),
49 (downstream exon)
Score:
31TAGAGGAAGATTTCACTCCTAAAGTGACCGATTTTGGTTTAGCAAGGGAAGCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
Block sizes:
36 (upstream exon),
39 (downstream exon)
Score:
7TAGAGGAAGATTTCACTCCTAAAGTGACCGATTTTGGTTTAGCAAGGGAAGCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
Block sizes:
44 (upstream exon),
49 (downstream exon)
Score:
32TAGAGGAAGATTTCACTCCTAAAGTGACCGATTTTGGTTTAGCAAGGGAAGCATCCAATGCGACTCAACCTATATCTACCAGGGTAATGGGTACTTTCGGgtaaggcaca ... gactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
ctttgac putative branch site (score: 32)
ttttatttttttttct CT-rich tract
tttttatttgactcga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-tcgtgct
- - - - atcacaa
- - - - - - - - - - - - -cctacac
- - - - - - - - - - - - - - - - - - - -acagcag
- - - - - - - - - - - - - - - - - - - - - - - - - -tgctttt