Sequence
atgc intronic sequence ATGC exonic sequence...cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 3
-cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
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tcttactgt-tctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatat-----tttgt-actggt-ttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
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----tatcctttgagtagtgtgccactgact--attttattagg-actgatcatcctttgtttctcttcaaatttgatataatataattctctgtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
cttatgatatctaagcaattgatttg--cgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattt-tatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
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ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattatttgtttcct---tatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatctttt--actggatttgt-gcatatct-gattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
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--taatctaacggatcag--gagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 2
cttatgatatctaagcaattgatttgcgactccatgtttttaaatgt-tgatcttttactggatttgtgcatatctgattttatattttgtactggt-ttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
| | || | | |||| | | || ||| || | | | ||| || | | | |||| || | |||| | | ||||||| |||||||||||||| |||||||| ||||| || ||||| | |||||| | || |||||||| |||||||| || ||||||||
-atccactttccatttgagcaattttcaaatc-atgcttaagtttccgcaaacctttgctttgtataccctatcttgataccatcatctgtattactattagTGATAGTGGTGAAATGTGCGCAATGAAAGAGGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAGAGTGCAAAGCAATTGGGGCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 4
--------ctta--tgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttac-tggat-----ttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
||| | | || | |||| | ||| | |||| | | | | | || ||||| || | | ||| | || || || |||||||||||||| |||||||||||| |||||||||| || || |||||||||||| | ||||| | ||||||||| || || || |||
gtatgtattttagttaaaatgttcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 4
--------ctta--tgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttac-tggatttgtgca-----tatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
||| | | || | |||| | | ||| | |||| | | | | | | ||||| | | | | ||| | || || || ||||||||||| || |||||||||||| |||||||||| || || |||||||||||| | ||||| | ||||||||| || || || |||
gtatgcattttagttaaaatgttcttaatttctcatttattcctttttttaatctatcatttctacatatggatcttaataagaattgctttgtttaaaatgtttgtctcttttagTGAAAGAGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCGAAGCAATTTATGCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
---------------------cttatgat-atctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
| |||| || | | || || | | || |||||||| | |||| || | || | || | || |||| ||| | ||| |||||||||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || || |||
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttt---tttatacttttaaat-ccattagtttatacatcttataaattgtttggttaaaatgttgtcctg-tgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
-------------cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggat-----ttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
| | ||| || | || | | ||| || | | ||| ||| || || || | || | || | || |||| || | ||| |||||||||||||||||||| ||||| ||||| || || |||||||||||||| || || || || ||||| || || || |||
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatg-tgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
atctgat putative branch site (score: 4)
atatctgattttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - ctaagca
- - - - - - - - - - - - - -gactcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcata