Sequence
atgc intronic sequence ATGC exonic sequence...tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 11
----tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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agctcatctattagtctggcttggtttagtagttacgtcatgcta-ggcttctcagaaaacagattgttgacc-ttttgtt-taaaatggttac-ctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTG
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
-tctgatttggttcaaca-ttacatgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaaga--aattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 3'ss of exon 12
tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaacataatt-tttggatgaccattttgttataacaacattgtgtttttt-----cagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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---atgttagttgtac-ttgcaggctggcattctctt--tcttgatatgtctatggtcatctgcatctgaattttgctcgactgatattgggttctgtgggtgcagATAAGGACACTGAGAGGACATACCAACGAAAAGAATTTTGTTGGGCTATCTGTTAACAGTGAATATATAGGTTGTGGTAGTGTAACAAATGAGGTGTTTG
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S154_52V6.1 (Physcomitrella patens), 3'ss of exon 11
-tctgatttggttcaacatta---catgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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cttttatctatttacttatttatttttgactcatttggggtatacccaatgcattagtgagttaaggtgtcctaagtttttgaagt----tgatcatactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 11
tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaac-ataatttttggatga---ccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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--ctatgtagcacaggtcgggcttctctttgttgagtattg--gttatgtacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG
upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 11
tctgatttggttcaacattacatgcccaatttgaaatagtgcagc-tacgaacataatttttggatg--accattttg----ttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
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-------tgcggagacatgccatatacattcgaaggagacaaagtatttaaacggcaatattgcgtgccatcgtattgcaatttctgatataatattcctcttgcagGCACGAACATTCAGAGGACATACCAATGAAAAGAATTTTGTAGGTCTGACTGTAAATAATGACTACATTGCTTGCGGCAGTGAAACGAATGAGGTCGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
ttataac putative branch site (score: 2)
tgttttttc putative PPT
attttgttataacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG