Sequence
atgc intronic sequence ATGC exonic sequence...gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
---gtgtttttttccctcatgtttcc---cccttttgccttccttgttttccta--tcacatctttac--cttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
|| | | ||| | | | | | | | || || | | | || ||| || |||| || | | || | | ||||||||| ||||| || |||||||| || || || ||||||||||| |||||||| ||||| || | ||| |||||| | ||||
gtagtagctagcagcgccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
----gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttacctt----ctttttttttttctttttcctgttttat-----gtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
|| | || | | | ||| || || || || | | | || || || | | | | ||||||||| ||||| || || ||||| || || || ||||||||||| |||||||| ||||| || |||||||| || ||||||
gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
--------gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
| | || | ||||| | | || ||||||| || | | | | |||| | | | ||| ||||| ||||| || |||||||||||| ||||| || ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||
tgagcaatgagcattctcaactcat---ttaactgttcatcttcctttttgtgtt-ttgtgt-tttatgatttctctttatttctaaagggtgttt---gtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
| | |||| | | || |||| | | | ||| |||| | ||| || | | | | ||| |||||||||||| ||||| || ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||
gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctg---ttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
| || | | ||| | || | | | | || || | || |||||| || ||||| | | ||| | ||||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| || ||| | ||||||||||||||||
---tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttcttt--ttcctg----ttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
|| |||||| | || | | ||| || | | |||| || ||| | |||| |||| || || | | ||| ||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||| || ||| | ||||||||||||||||
-----ttaagtgttcatgtaagagcaattccaacaacatatttgactgtt-tacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatct-ttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
||||| |||| | | || | | || | ||| || | | | || |||||| | ||| ||||||||||| ||||||||||||||||||||||||||||| |||| |||||| ||||| || || || |||||||| ||||
--------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
tctttaccttcttttt CT-rich tract
tttttttttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - ttccctc
- - - - - - - - - - -ccccctt
- - - - - - - - - - - - - - - -ccttcct