Sequence
atgc intronic sequence ATGC exonic sequencegttggtcattaatttccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
-----------------gttggtcattaatt-tccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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gtatgttgaaacaaatgaattaccatgctttgttcagaataatcctcttcctggcttgtatgggatctaacat-gccatgcattttt-atttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
--------------------gttggtcattaatttcc-----ttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatat---tactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
----gttg-gtcattaatttccttaatgtctttgtttgt---tgtatttattcatcttttc------attggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------gttggtcattaatttccttaatgtc-tttgtttgttgtatttat--tcatcttttcattggcatgtatctttgatgaa-tagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttg-cgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------gttggtcattaatttccttaatgtctttgtttgttgtatt-tattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatt----tgtagcggtggtg--cagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 9
-gttggtcatt---aatttccttaatgtctttgtttg-----ttgtatttattcatcttttcattggcatgtatcttt------------gatga-atagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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cattagtaattctaactctactagatgactgaacggggcagttggtgtctaccaagaaagttattaaaacctgtctgcctgtgttgtaacggtgatacagGTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gttggtcattaatttccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaat--agGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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----------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gttggtcattaatttccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaat--agGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
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----------------------------gttggttgttttcgtttgacaagttacatacatgactcttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGMapped 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|110371471|gb|EC935522.1|EC935522EST: TTGTTCCTGTTGATGAACACATGCAAGTAATTGATGCAGATGGAAAGCTG GTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCT
genomic: TTGTTCCTGTTGATGAACACATGCAAGTAATTGATGCAGATGGAAAGCTGgttggtcatt ... tgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
ctttgat putative branch site (score: 5)
tatcttt CT-rich tract
tatttattcatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtcattaatttccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA