Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 18
gtaagttgact--ctgaacaacggcaaaaaaattct-gcaaccttttttt----aaaagt-taatacttaatttaatcagGTATGGTTTTCTTCT---TGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
|||| | | | |||||| | | | |||| | ||||||| || || | | ||| | || |||| ||||||||||| |||||||| ||||||||| ||||||||||| ||||| |||||||| |||||||||||||| ||||| |||||||| |||||||||||||||
gtaaataaaatatttgaacagtagtattgcatttctagttaccttttattttgcaatactgtaacagttcattttatcagGTATGGCTTTCTTCTTCTTGAGGATGTCGCATCTCAAGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 19
--------------------------------------------------------gtaagttgactctgaacaacgg----caaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCT---TGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
|| | | | | | || | ||| | | || | ||| | | | |||||| |||||||||||||| ||| ||||||| ||||| |||||||| |||||||||||||| ||||||||||| ||||||||||| |||||||||||||||
gtataacaacagagaaagaaactatggtgattgatatcctttcaaattacccccccgtcccctatcccctatccccgtgctttttgcacatttctaacctttctgttattgacttgggagtggta-aatcagATATGGTTTTCTTCTCCTTGAAAATGTTGCCTCTCAGGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAATTCAACATTTTGCCTGAGATGTATCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 17
-------------------------------------gtaagttgactctgaac--aacggcaaaaaaat-tctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCT---TGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
|| || | | | | | | | | ||| ||| | | | | | | |||||| |||||||||||||| ||| ||||||| ||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||||
gtagaacaacaaagaaactatggtgattgatatcctttcaaattagtccccatcctagtgttttttgcacgtttctaacttttctgttattgatttgggagcggtgaatcagATATGGTTTTCTTCTCCTTGAAAATGTTGCCTCTCAGGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 17
---------------------------------------------------gtaagttgactctgaacaacggcaaaaaaat-tctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCT---TGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
| || |||| | | | || | | | |||| || | | | | || |||||| ||||||||||| || ||| ||||||| ||||| ||||| || ||||||||||||||||||||||||||||| || ||||| |||||||||||||||
gtataataacagaaaactgatgatttatatcctttcaaatactatcaccttccacattccttctgccctggtgtttttacatgtgtctatccttgttcttattggcttgggtgtgttgaatcagATATGGTTTTCTCCTCCTTGATCATGTTGCTTCTCAGGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 19
----------------------------------------------------gtaagttgactctgaacaacggcaaaaaaat-tctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
| || ||| | | | || | | |||||| || | | | | ||| |||||| ||||||||||| ||||| ||||||||||||| |||||||| |||||||| |||||||||||||||||||| || ||||| | |||||||||||||||
gtataacgacagaaagactgataatttatatcctttcaaatactatcaccttccacattccctccgccctggtgtttttgcatgtgtctaaccttgttcttattggcttgggtgcattgaatcagATATGGTTTTCTCCTTGATAATGTTGCATCTCAGGATCCACTTAGTGTTTCGGTTGCAATTCTTCATCAGTTTAATATTTTGTCGGAGATGTATCAAGTT
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 19
--------gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatca-------gGTATGGTTTTCTTCTTG---AGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
| | | | | | || | | ||| | ||| || | | | || | | || |||| | |||||||||||||| | || | |||| | |||||| || |||||||||||||| ||||| |||||||| || || || || ||||||||||||
gtgacaatgccattcatcattagtagttgtgcaagggaccgtacaagcgtttcttcataagttttaatcacattgatcatattgcagATATGGTTTTCTTCTGGTGGAGAACATTGCTGATAGAGATCCTCTAAGTGTTTCAGTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTG---AGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT---------------------------------
||| || | | | | || ||| |||||||||||||| | || | |||| | |||||| || |||||||||||||| ||||| |||||||| || || || || |||||||||||||||
-------------------------------------------gttttaatcacattgatcatattg--cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 19
-------------------------------------------------------gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTT---GAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
|| | | | | | || | | | || | | || | | || | ||||||||||| ||||| ||| | ||||| | ||||||| || |||||||| ||||||||||| |||||||| || || || || |||||||| |||
gtaacaactccatctccagttggtgcactttcattgtattgcatgtcctcttataataggcttcccatactttttagttgcaataatgttgaatggtcatgctgtttttcttttgtcatact-ttagGTATGGTTTCCTTCTGCTGGAGAACATTGCAGCAAAAGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAA---
upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------------gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTT---GAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
||| | | | | | | | || | | || || || | |||||| | |||||||||||||||||| |||| ||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||| | |||||||||||||||
gtacacatagatgacaaggttttattatctagttgtattgcacttataaattttgtattcttttcttaagaatctgtttttattttattttattttcccttgt---ttggttgttaatt-gaccagGTATGGTTTTCTTCTACTGGAGGGTGTTGCATCTCAAGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAA---Mapped 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|76924723|gb|DV170102.1|DV170102EST: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCG GTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
genomic: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
EST:
gi|32934067|gb|CF038879.1|CF038879EST: TCAAGATCTGGGTATCCAACAAGAATGGCTCACCAGAAGTTTGCTCGGCG GTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
genomic: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
EST:
gi|211293264|gb|FL097156.1|FL097156EST: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCG GTATGGTTTTCTT
genomic: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTT
EST:
gi|32935299|gb|CF040111.1|CF040111EST: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCG GTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
genomic: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
EST:
gi|74243522|gb|DT651436.1|DT651436EST: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCG GTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
genomic: TCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTC
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:
49 (upstream exon),
28 (downstream exon)
Score:
206TTGTGCTTCAACAACTTAAATGTTGTGGGGTTCTTGAGGTTGTCCGGATTTCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
Block sizes:
49 (upstream exon),
28 (downstream exon)
Score:
128TTGTGCTTCAACAACTTAAATGTTGTGGGGTTCTTGAGGTTGTCCGGATTTCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
Block sizes:
49 (upstream exon),
28 (downstream exon)
Score:
113TTGTGCTTCAACAACTTAAATGTTGTGGGGTTCTTGAGGTTGTCCGGATTTCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
Block sizes:
49 (upstream exon),
28 (downstream exon)
Score:
194TTGTGCTTCAACAACTTAAATGTTGTGGGGTTCTTGAGGTTGTCCGGATTTCAAGATCTGGGTATCCAACAAGAATGACTCACCAGAAGTTTGCTCGGCGgtaagttgac ... atttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
acttaat putative branch site (score: 194)
aacctttttttaaaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG