Sequence
atgc intronic sequence ATGC exonic sequence...ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtatttatggtttttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G374574_T02 (Zea mays), 3'ss of exon 2
------------------------------------ttcctttgccaaattttattgccataatgatgtcaatgt----tacagaaaatttcccattgcctgcctgcttatagtattt----atggtttttgtgatggaaa-----------------cagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
|||| | || | || || || || | || | || | | || ||| ||| ||| ||| | | ||| | | | | |||||| | ||||| ||||||||||| |||| ||| |||||||||||||| ||||||||||| || || ||||| || || || ||||| || ||||||||||
gtggtgccttccctttgtcttcttcttcctcgttttatcctgtatcatcgctcatcctcactatcatctaaaaatgaaatatgatcagtcatcctctgcatgcatgcccttagccccttaccaaggtgctgctaacacatttactttactcgcctgctcagTCTCTACAAGCCCTTAAGAAGATCTCTCTGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCCCTAATGGCTGTTCTATCGTATCTCGACTTCTTCTCCA
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 1
ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttcccattgcctgcctgctta--tagtatttatggtttttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
| || || || |||| | || | | | ||| || || | || || |||| | | | | | |||| |||||||||||||| || ||||| | ||| || |||||||| |||||||||||||| ||||| |||||||| || ||||| || || || |||||||
-tatgcatacagataatagacgcatacgtgtaccatctctttgtatttgtatgcatgctcttgatggtggcctaacatatatgctacgttttttt-atttagTCATTGCAAGCTCTTAAAAAAATATCCCTGGAGCATCCAACTGCGTGCTTGCGAGCTGGTGCACTAATGGCAGTCCTATCATACCTTGACTTTTTCTCCA
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 1
ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtat--ttatggtttttg-tgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
| ||| || | |||| | | | | ||| | | | | | | | |||||| | ||| || |||| || ||||||| | |||||||| ||||||||||||||||| || || ||||||||| | ||||| || || || ||||| |||||||| ||| |||| ||||| || |
--cagttgtagaagaattatgcctttttttt-ttaatctaagacttagcattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 1
-----ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttccc---attgcctgcctgcttatagtatttatggtt----tttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
|| || ||| | | || | | |||| | | || | | | | | | ||| | | | || | | || ||||| | |||||| | ||||| || |||||||| |||||||| |||||||||||||| | ||||||||||| || ||||| || ||||| || |||| |||||||| |
gttattttctcactcaatctcttttatgcctttagttattatgtatctggaattctttttagaattttgtcttactttgaattctgatagatgtgattgttgatgtgagcagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTCGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCGA
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------------------ttcctttgccaaattttattgccat----aatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtatttatggtt----tttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
|| || ||| | | || | || || || | | | | | | | | | || ||| | | | || ||| || ||||| |||||||| | ||||| || |||||||| |||||||| |||||||||||||| | |||||||||| || ||||| || ||||| || |||| |||||||| |
gttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttt-tctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
-----ttcctttgccaaattttattgccataatgatgtcaatg--ttacagaaaatttcccattgcctgcctgcttatagtatttatggtttttgtg-atg------gaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
| | |||| || || ||| | || || |||||| || | | ||| | | | | || ||| || ||| ||||||||| |||||||||| || |||||||||||||| |||||||||||||| ||||||||||| || || ||||| ||||| || |||||||||||||||||||
gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcac--acttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttcccattgcctgcctgcttatagtatttatggtttttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
ttatagtatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtatttatggtttttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - ccaaatt
- - - - - - - - - ttgccat
- - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - -cagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgcc