Sequence
atgc intronic sequence ATGC exonic sequence...aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 2
--aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttg-------acgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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tgaactt--ttattttttttattcat-ataataacacaagtt-gctgaataattctacgggaaaaaaagcatcgtcctggtcctcacaaatatttttccatc-----agTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 2
-aactgaatgatctgttgaatccatgacgccaatcccttctagtt-tgatacttctttgacgtataatcaagattctcacagacgtttcctcacct-caccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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tcactgaattgatacttcaatc-ataatg--gatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 2
aactgaatgatctgttgaatccatgacgccaatcccttctagtttg--atacttctttgacgtataatcaagattctcacagacgtttcctca-cctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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---aaaatgaactcatacttcaatcaaaatggatttaattgaatggctatgcttgcttctcttagactgactttaatttcaatttattctttaaccgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATAATATCACTAG
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 2
aactgaatgatctgttga-atccatg-acgccaatcccttctagt-ttgatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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aagcgtactttctctccatattgacatgcattaaaatgtgcagttatttatcttttcttgaggtaggttttgctgatttgataattttttcttgtgtca---gGTTCCAGGTAAAAAAGAAGCAGTTTTTCCGAAACTTTATGACAATCATATTGTTTGGTGCTATTGGTACACTGATATCCTTTGGCATTATATCTCTAG
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 1
---aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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attgttcaagtaagatcctgtattcactgatatgagacttgatgattttagcgctctgtgat-tgcagtccgg-tgatgactcgaatatggttgtttc-tcagGTTCCAGGTGAAGAAGAAGGAGTTCTTTCGGAATTTTATTGCTATCATGTTATTCGGAGTCATCGGAGTCTTCATTTCTTTCGCAGTTATTTCAACAG
upper sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 2
-------aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
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cggcataaattggattgcttcttgtgttgatggatgtgcaacttcaaagcttgcgtctac----acttaaaattcag-tgacgacatgacttttgtgattct--cagGTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTTTTTTGGAGTTATAGGAGTCTTTATTTCTTTCGGAATTATCTCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
tcctcac putative branch site (score: 2)
tttcctcacctcacc CT-rich tract
tataatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttgacgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- ctgaatg
- - - - - -ctgttga
- - - - - - - - - atccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacagac