Sequence
atgc intronic sequence ATGC exonic sequencegtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 10
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
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----------------------------------------------------------ctctcccccatctttttgaggtgttatttgttgtttgtcaatagtc--aatactgagaaggaaaaggacagacagagta-attatgtattcttcccttg-tcagATACTACTCAAGTTTGGAAGTAGCGTCAGAGTACTTCAGGTCTGGTGCTGACAAGATTTCAATTGGTAGTGATGCCGTTTTTGCTGCTGAAGCCTATTTG
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 13
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttat-cttttatttttttttattaaatgttaattctccttcagtgattttcttgag-atgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
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------------gtattattact--gatcattatggagattatgctattgactttcttgcattctttcccctctattgaa-attattcagtctt--atagttttatcaattgtgttccctcagaattttcaaatctttttgatccga-tcaattatattctcagGTACTATTCTAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttat-ttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgag-atgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
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------------gtattattatt--gatcattatggagattatgctattgacattcttgcatttttttccctctattgaa-attattcagtctt--atagttctatcaattgtgttccctcagaattttcaaatctttttgatccga-tcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 12
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttt-tatttttttttattaaatgttaattc-tccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
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--------------------------gtacatgttaatcttttc-agcctgtttctgtgaacatgtctgtgcaggcattatgttcttttatatttcagcaaggactttgcaatttttattccctacaaca-----atttaacatcaagttaatttgg--ctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
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-------------------------------------------ttcctcacatgttaagccgaacttttcatcactcaat---------cctgtatttaatctgttcaa--gagattgaagtactct-----catcaacttt---gtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
ccaatctcttcctc CT-rich tract
aactattatggataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA