Sequence
atgc intronic sequence ATGC exonic sequence...gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaagatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G34820.1 (Glycine max), 3'ss of exon 2
----gcaaa---taaacagaggtcttt--ttgtt--------tttccttttttgattaaattcaaagat-ttctttaatactgtttggatgattgatatctcaatggtttccttga-agGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
||||| |||| | | || ||||| || ||| || || || | || | || || | || | ||| ||| | ||| | | | || || ||||||| ||| |||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||||||||| |||
gtgagcaaaatgcaaacttggcttttgaattgttaaaggcacttctttttagtgttttaaacaataggtcttacttggaagtgatgcttatgttgttattttgatgactgtttcggcagAGTGTGAAGGTTAATTTGATAATGACGGATTATTCCATGCCCGGGATGACAGGATATGAATTGCTCAAGAAGATAAAG
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G10170.3 (Glycine max), 3'ss of exon 2
gcaaataaacagaggtctttttgtttttccttttttgattaaat-tcaaagatttctttaatactgtttggatgattgat-atctcaatggtt-tccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
| || | || | ||||| | || | ||||| || || | || || | || || | ||| | | | | ||||| | || || || | ||||| ||||| || |||||||| ||||| ||||| ||||||||||| ||||| || |||||||| ||||||
gtaagtgaattctg--cttttgggttattggcttttgtttggatgttggttgttgaatt--tggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G19870.2 (Glycine max), 3'ss of exon 1
gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaagatttctttaatactgtttggatgattgatatctcaatggtttccttga-agGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
| || |||| | ||||| || || |||| || | | | || ||| ||| ||| | ||| || |||| || || || | || ||| |||| |||||||| ||||| ||||| ||||||||||| || || |||||||| ||||| |||
gtaagaaaacttgg---cttttgaattgttaaaggcacttcttttcaggttactcggaagtgaagctt--atg-ttgttattt-gatgattgttttgacagAGTGTGGATGTTAATTTGATAATGACGGATTATTCCATGCCGGGGATGACAGGATACGAATTGCTCAAAAAGATTAAG
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaagatttctttaatactgt-ttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
| || || | || || || ||||| ||||| | | | | | | ||| || || | |||| | | | || || ||| | ||||| | ||| |||| |||||||| || ||||||||||||||||| || ||||| | || |||||||||||
gtaataaatctga--tcattgtgtttaatatttttg----agagtgagaatccattcaaatttggtgttaaaagatttttggtttga-aattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S94_88V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------gcaaataaacagaggtctttttgtttttc---------cttttttgattaaattcaaagatttctttaat---actgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
|||| | | | || | | | | ||| || | || | || || | | ||||||| ||| || | ||| || | |||||||| |||||||||||||||| |||||| |||||||| || ||||| | ||||| | | |||
gtaagtattttttttgacgtttaaatttctaaaatatgtattatctcacaagcgaaaatacatacgatgtgatgctgttgctttgtgaagtgaaccatgtaactgattgaattcttcat--ctcatttgcagAAAGGGGCTGTGAATCTTATCATGACGGACTATTGTATGCCGGGGATGACTGGATATGACCTCCTCAAAATTGTGAAG
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------------------------------------gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaa--gatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
| | | || || | || | ||| | |||||| | | | | | | | || || ||| ||| ||| | || | || ||||||| |||||||||| |||||| | |||||||| ||||| ||||||||||| |||||
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttt-tgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
upper sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ14701 (Selaginella moellendorffii), 3'ss of exon 2
gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaa--gatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
| | | || || | || | ||| | |||||| | | | | | | | || || ||| ||| ||| | || | || ||||||| |||||||||| |||||| | |||||||| ||||| ||||||||||| |||||
-tgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttt-tgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaagatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
gattgat putative branch site (score: 4)
tttcctt putative PPT
atttctttaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaagatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- aaataaa
- - - - - - - - - - - - - - - - - - - - aaattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaatg