Sequence
atgc intronic sequence ATGC exonic sequence...caattcttcctattggcaggagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44450.2 (Oryza sativa), 3'ss of exon 1
-caattcttcctattggcagg--agtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAGAAGAA---TAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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tagattatgtctgaatataggttactgatcggtataagaaatgctcgttctttgtttcctgaacaaaattcacgtgctgagcttgcgtgatcaatt---gcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGAATCCAAGGAGAAGGGCAGGAAGTTCACCGAGACCGTTGAGCTTCAGATT---
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 3'ss of exon 2
-caattcttcc----tattg-gcaggagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAG---AAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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tagattataccagagtatggtgcactgattgatgagtatcagaaatgttctttcttttcc-ata-acaaattctgaatgtgagcttgtgcg-atcaatt---gcagTAAGTTACAAACCGAGGCTCTCAAGGAAGCCATCTCCCAGGTTGTTGCTGATTGCAAGGAAAAGAACAGGAAGTTCACCGAGACCGTTGAGCTTCAAATT---
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 3'ss of exon 1
----caattcttcctattggcaggagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAG---AAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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atggggagttttagggtttttagtagggtttgattggtagctacaacctactagtcgaattacacgtttaacggtcgtgttatgctgctctcgg----ctgcagTAAGCTTCAGAGCGATGTCCTCAGGGAGGCCATCACTCAGATTACCACTGCCGCTAAGGAGAAGAATAGGAAGTTCACAGAGACTGTGGAGCTTCAGATC---
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 1
caattcttcctattggcaggagtatttggaattctagagtattgttcccatccagatagatt--atctctgcctaataaat-tctacccattgatt--attgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAGAAGAATA---GGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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---tgagttctgct--ttggaaatttagttcctgtggtgagttgtttaatggttgttaggtttaatttgtagctgacggacgtggaatgattttttcggacgcagTAAGCTCCAGAGCGATGTCCTCCGGGAGGCCATTACGCAGATCACCACTGCGGCCAAGGAGAAGAACCGGAAGTTCACTGAAACTGTAGAGCTTCAGATT---
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 1
caattcttcctattggcaggagtatttggaattctagagtattgttcccatccagata-gattatctctgcct--aataaattctacccattgattattg-cagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAG---AAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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-gtcaggtaacacgaatatgaaatcttggaaattaggtttacgactctggtactgttttgatgatatggaactgaaatagagttta---atgtattctcaacagTAAGCTTCAGAGTGATGTTCTGAGGGAGGCGATCACTCAGATCGTGGCTGCAGCCAAGGAGAAGAATAGGAAGTTCACAGAGACTGTTGAACTTCAGATC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
taataaattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattcttcctattggcaggagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctacccattgattattgcagTAAGTTGCAGTCCGAGGTTCTCAAGGATGCCATCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - -gcaggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgccta