Sequence
atgc intronic sequence ATGC exonic sequence...gcaaggtgttttatattgatgtaaagtgatgttcgcttgcatggttgtctgctttgtcaccaatacatcctgcaataactacattatatgtatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G099598_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------gcaaggtgttttatattga-tgtaaagtgatgttcgcttgcatggttgtctgctttgtcaccaatacatcctgcaataactacattat-------atgtatgttgt---agGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
|| ||| ||| | || | || | || | | || | | || | | | | ||| | ||| | |||| || |||||| || || | |||||||| || ||||||||||| ||| |||| ||||| ||||| |||||||||| ||| ||||| | |
gtaacatatgatttgtctatgacaaacttagccttctttgaattgtttagtcagggtatttagaagtgggtatacatgacagtacatgctatttactgaaaatagaatggctaacattttc-gtaatgatgggatttccatggcaacctatgctgcttcagGAAGAGTAACATCAGAAAGTGTCATATTCAGCTTTGGCACTATACTGCTGGACCTCCTAAGTGGAAAGCGTATACCTCCTTCCCGT
upper sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G026767_T03 (Zea mays), 3'ss of exon 4
-----gcaaggtgttttatattgatgta---aagtgatgttcgcttgcatggttgtc-tgctttgtcaccaatacatcctgcaataactacattatatgtatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
| ||| | ||||| | |||| ||| | | | | ||||| || | || | ||| || || ||| || ||| ||||||||||| |||||||| || ||||| ||||| ||||||||||| || || || ||||| || | || || || |||
tccttggtctctgtctgtcattgaaatcaataagtaatgcaaacaaaaaagcaagaaatgcttcatctgtattattttctgaggaaa----gttttat-----tttcagGCAGGGTTACTCCAGAAAGTGTCATTTTCAGTTTTGGCACTGTACTTCTTGACCTTCTCAGTGGGAAACGCATACCGCCTTCACAT
upper sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------------------gcaaggtgttttatat-tgatgtaaagtgatgttcgcttgcat--ggttgtctgctttgtcaccaatacatcctgcaataactacattatatgtatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
|| || |||| ||| | | || | || || | | || || | | | ||| || | || |||| | | |||||| || || | |||||||| || ||||||||||| ||| |||| ||||| ||||| |||||||| | ||| |||||| | |
gtagcatacgatttatctatgacaaacttagccttctttgaattgtttagttagggtatttagccgtgatatacatgacattacatgctatttactgaaaatagaatggctaacattttcctaatg-atgggatttccatggcaacctatgctttcttcagGAAGAGTAACATCAGAAAGTGTCATATTCAGCTTTGGCACTATACTGCTGGACCTCCTAAGTGGAAAACGTATACCTCCATCCCGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|34543647|gb|CF511879.1|CF511879EST: AAGTTACAGCACAAATCTTGCCTATACACCTCCTGAGTATCTAAGAAATG GAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTCCTTCTGG
genomic: AAGTTACAGCACAAATCTTGCCTATACACCTCCTGAGTATCTAAGAAATGgtaaagaatc ... tatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctgctttgtcaccaatacatcctgcaataactacattatatgtatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
caataac putative branch site (score: 2)
aataactacattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaggtgttttatattgatgtaaagtgatgttcgcttgcatggttgtctgctttgtcaccaatacatcctgcaataactacattatatgtatgttgtagGAAGGGTTACTCCTGAAAGTGTTATCTTCAGCTTTGGGACTGTACTTCTGGATCTCCTTAGTGGAAAGCATATTCCTCCAAGTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - aaagtga
- - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgca