Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcctcgtatctcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------gtaatgcctcgtatctcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
|| || | || ||| | || |||||| || ||| ||| | || | || | ||||| |||||||| || ||||| || |||||||||||||| ||||| || | ||||||||||||||||| || |||||||| || |||||||||||||| |
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagatt-ttgtttttttgtt--tcgctgctgcggcggtggggcttg-tacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 1
-------------------------------------------------------gtaatgcctc-gtat-ctcaaatcttattg-----tttattggttattcgtttcttaatctcctctctttactt-cagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
| | |||| || | | | | | ||| | | ||| ||| || || | | | ||| ||||| |||||||| || |||||||| |||||||||||||| ||||| || | ||||||||||||||||| || |||||||| || |||||||||||||| |
gtccaggagggcgtcgatgtctttgacagcatctggaataaggcacgcccccagcgccctccctccgtttacccggcccctgccagaactttttctcgcgatt--tttgttgattttttttgtttgggggcagGTCTACGACACTGAGAATGCCAACCAGAAGGAGAAGTTCGAGGCGGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 1
----gtaatgcctcgtatctcaaatcttattgtttattggttattcgtttctta-atctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
|| || | || ||| || | | | || | | || || | | | | | | | ||||||||||||| ||||||||||| |||||||||||||| |||||||| ||||||||||||| ||||| || ||| |||| || |||||||| |||||||
gtaggtcattcttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttagGTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACAT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 1
gtaatgcctcgtatct----caaatcttattgtttattggttattcgtttctta-atctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
||| |||| | ||| | | | || || | | || | || | | | | | | | ||||||||||||| |||||||| || |||||||||||||| ||||| || ||||||||||||| ||||| || ||| |||| || |||||||| ||||| |
gtaggtcctcttctcttcttcgattatttcgaattttctcctgtttttggctcacacatggcgttggtgcgttagGTTTACGACACCGATAATGCGAACCAGAAGGAGAAGTTCGAGGCGGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACTT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G04690.2 (Glycine max), 3'ss of exon 1
---------------------------------gtaatgcctcgtatctcaaatcttattgtttattggttat--tcgtttcttaatctcctctc---tttacttc------agGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
||| | | | | | ||||||| | | || | | | ||| || | | ||| || ||||||||||||| || ||||| || ||||||||||| ||||| || || | ||||||||||| ||||| || ||| |||| |||||||| || ||||| |
gtacttcatttgtttctctcactttttttttatttaaaagttttcagtttttgt-tcattgtttttagattttcattgcttcggaacaaaatgacgggtttggtttggggatagGTTTACGACACTGACAATGCTAACCAGAAGGAGAAATTTGAAGCGGACCTCAAGAAGGAGATTAAGAAGCTCCAGAGGTACAGAGACCAAATTAAGACTT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G18230.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtaatgcctcgtatctcaaa----tcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
|| ||| | | ||| | ||| || | || | | || | | | ||||||| || || || || |||| ||||| ||||| ||||||||||| || ||||||||||| |||||||| || ||||||||||||||||||||||||||||
gtgagcagaatgtttgttttcgaagcagaaaagttttttactggacagaggaaaaactcggtttcggacttttttggtgtttcagGTATATGATACAGACAATGTTAATCAAAAGGAAAAGTTTGAGGCGGACTTGAAGAAGGAAATCAAGAAGCTGCAGCGGTATAGAGACCAGATCAAGACAT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------gtaatgcctcgtatctcaaa----tcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
|| ||| | | ||| | ||| || | || | | || | | | ||||||| || || || || |||| ||||| ||||| ||||||||||| || ||||||||||| |||||||| || ||||||||||||||||||||||||||||
tttatgcagtggaatgtgagcagaatgtttgttttcgaagcagaaaagttttttactggacagaggaaaaactcggtttcggacttttttggtgtttcagGTATATGATACAGACAATGTTAATCAAAAGGAAAAGTTTGAGGCGGACTTGAAGAAGGAAATCAAGAAGCTGCAGCGGTATAGAGACCAGATCAAGACAT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S134_165V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------gtaatgcctcgtatctcaaatcttattgtttattggttatt--cgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
|| | | | | | | || | |||| | | | | | || || |||||||||||||| || |||| ||||||||||||||||| ||||| ||||| |||||||| || ||||| || ||||| ||| | || || || |||| |
ttccttactcacgtcatgggcaggtaatgtggttggttgattttgctgacacatctctccacggttctcaacaatgacgtaacatgtcgaggtatcgcagGTTTACGACACTGAAAATGTTAATCAGAAGGAGAAGTTCGAGGCAGATTTAAAGAAGGAAATTAAGAAGCTACAGCGTTATCGTGATCAAATTAAGATGT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 3'ss of exon 2
------------gtaatgcctcgtatctcaaatcttattg-----tttattggttattcgtttcttaat-------------ctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
| | | | | ||| | | | ||| |||| ||| | | || | | | | | ||||| ||||| || || ||||| ||||||||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| ||| | || || ||||||| |
gacattgaattactcagatcatggacaattaatatcgtcggtggtttttctggtctttctctccgtagtgctgacgaagaaacacgttgaggtgtcgcagGTGTACGATACTGAAAATGCAAATCAGAAGGAGAAGTTCGAGGCCGATTTAAAGAAAGAGATCAAGAAGCTACAGCGTTATCGTGATCAAATCAAGATGT
upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 1
gtaatgcctcgtatctcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
| | | | | | | | | || ||| | ||| | | | || ||||| || || || || ||||| ||||| ||||||||||||||||| ||| | |||||||| |||||||| || ||||| || || |||||||| ||||| |
-----gtatggaaatcta--tggcgtcgcctcgccattgatcgatcgagaatttttttttcttctcgcagGTGTATGATACCGAGAATGCAAATCAAAAGGAGAAGTTTGAGGCCGATCTCAAGAAGGAAATCAAGAAGCTACAGCGATACAGGGACCAGATTAAGACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
tcttaat putative branch site (score: 3)
ttcgtttcttaatctc CT-rich tract
tcttattgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcctcgtatctcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA