Sequence
atgc intronic sequence ATGC exonic sequencegtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
| || | || || | | | | ||| || ||| | || | | || |||| || | | | | | |||| |||||||||||||||||||| ||||| |||||||| |||||| | ||||||||||| ||||| || ||||| || ||||||||||| || || |||
------gtatttcttattacaatgattttctttcatctgattgttattctgtactaaggcatcgtgg----taagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 4
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaa---aaaaatgaactaggcgattaagttgga-----tttcatgttgtatttct---ttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
||| | | ||| | |||| ||| | | || ||| | ||| || | | || | | ||| || || | ||| | ||| ||| | || | ||||||||||||| |||||||| || |||||||||| ||| |||||||||| | |||||||| |||||||| ||||||||||| ||||| |||
gtacagtatcattttgatttcaaagttaccgtgtgattt-tcgcttgtctataactataagcggtttgctgcattgagctgaagcgattttgttaatgtgtttttgcattgttcagCAAGTATGCCATCGTGACTTAAAGCTGGAGAACACTCTGCTAGATGGAAGTACTGCTCCTCGCTTGAAGATATGTGACTTTGGTTACTCGAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G138861_T03 (Zea mays), 3'ss of exon 4
-----------gtattcaa-acttttagtt-ttctgccttaacctctgttttat--tatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
|||||| | |||||| || | | | | | || || |||| | || | || ||| ||||| | | | || | | |||| |||||||||||||||||||| ||||| |||||||||||||| ||||||| || |||||||| ||||||||||| || || || || ||||||
gtaagctactgccattcaatggtattagttattatatagtggcatatcttccatcctattgttactgtttactcataccatgc-attgagttgagctgcctttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAACACACTTCTAGATGGGAGTGACGCTCCTCGCTTGAAGATTTGCGATTTCGGTTATTCCAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 5
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
||||| | || | | | || | || | || | |||| || | | | || | || ||| ||||| | | | || | | |||| |||||||||||||||||||| ||||| |||||||||||||| ||||||| || |||||||| ||||||||||| || || || || ||||||
gtatt---agttattatatagtggcatatcttccatcctattgttactgtttactcat---accatgc-attgagttgagctgcctttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAACACACTTCTAGATGGGAGTGACGCTCCTCGCTTGAAGATTTGCGATTTCGGTTATTCCAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 4
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttct-ttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
||||| || || | | || | | || ||||| | | | || | || ||| || || | | | || |||| | |||| |||||||||||||||||||| ||||| ||||||||||||| ||||||| || |||||||| |||||||| |||||||| || || ||||||
gtattagttgttatataatggcacatttttcatcatattgttatt-gttt-----actcataccatgc-attgagctgagctgccttttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 4
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
|| | | ||| | | || | | | || | | | | | | | ||| || || || | || || | |||||||||||||| ||||||||||| |||||||||||| |||| ||||| || |||||||||||||||||||||||||| |||||||| || |||
---------------gtacataagttcggcatctttagtctttact-cttacaataggtataatgagttgctgacttgaatgtctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGTTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCAAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 4
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
||| || | | || | ||| || ||||| || | | ||||| | || | | |||| || | || || | |||||||||||||| ||||||||||| |||||||||||| || | ||||| || |||||||||||||||||||||||||| |||||||| || |||
gtacataagttcggcatctttagtctttac-----ttttacaataggtat------aatgagttgctgacttcaat---gtttctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGCTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCGAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 4
----gtattcaa-acttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttc-atgtt-gtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
| ||||| || | |||| || | | || ||| | ||| | |||| ||| | | || | | | ||| ||||| || || || || ||| |||||||||||||||| || |||||||| ||||| |||||| |||| ||||| || || ||||||||||||||||||||||| ||||| || ||||||
gtatgaattcagcacatgtagtctt-tacttttaccagttatttgcttcccagaagaaagaaa-gcatgagatgtctgacttgaatttctatatttgtcttccttaatgaagCAAGTATGCCATCGCGACTTGAAGTTGGAAAACACATTGTTGGATGGTAGTCCTGCTCCTCGTTTGAAGATTTGTGATTTTGGCTATTCCAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 4
------gtattcaa-acttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttc-atgtt-gtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
| |||||| || | |||| || | | || ||| | ||| | |||| ||| | | || | | | ||| ||||| || || || || || |||||||||||||||| || |||||||| ||||| |||||| |||| ||||| || || ||||||||||||||||||||||| ||||| || || |||
gtacatgaattcaacacatgtagtctt-tacttttaccagttatttgcttcccagaagaaagaaa-gcatgagatgtctgacttgaatttctatatttgtcttctttaatgaagCAAGTATGCCATCGCGACTTGAAGTTGGAAAACACATTGTTGGATGGTAGTCCTGCTCCTCGTTTGAAGATTTGTGATTTTGGCTATTCAAAG
upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
|| | || | | | | || || | || ||| | || | | | | || | || || | || ||||| | || |||||||| |||||||||||||||||| || | |||||||| || || ||| | |||| || ||||| ||||| || || |||
gtaattgttctgaaccctgacgcgcgtggttttcctatcagcattgaagttttctggatttgtacagtgcttccttatgacctgactacaatttttctggtaacattttagCAAATTTGTCACCGTGATTTGAAATTGGAGAACACATTGCTGGATGGAAGTCCTGCACCTAGACTGAAAATCTGTGATTTTGGATATTCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
ttgtatttcttttt CT-rich tract
ttgtatttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA