Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 10
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggc-caaaactgtttggggggaccatatgactggaaa-----ctgttttttttagctaggatttgttcttg--gtctaat--ctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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gtaatgttctatgtttgctgagtttttctaa---atttaaatgcgttgttttgccaggctggtcatactatttttgtatgcaactctttgggggggattctgccttcctccttaggctagcgtttttctgcactatctaatgctaggtctctatgtgttcagATAGGATATCTTGAATATTGCAAGCAGCGTGGATTCACAAGCTGTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 10
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggt------ctaatctgttctcattgtg-------tacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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----gtaacctttagttctaattccttgtccttgtgttgggtggaatattatac-agccttg--tggaaccctttgttggagtcattcaagttctgatttgtttccttcctgtagttctattctatataaatagttgagtagttttcgttatgattttcttttagATTGGATACCTTGAGTATTGCAAGAAACGTGGTTTTACAAGCTGCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttgg-ggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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------------------------------------gtaaatttgg-acactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttc--ctgtaaattatatttgatatgaattatttctttt-----tagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgtttttttta--gctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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-----------------------------------------------gtaagtcctggtcttctgaaaccttggtgtttaaccaatatctgtgctttttactttctacactgtatggaggatctaagagtataatctgatcctttt---tatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcat-tgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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-----------------------------------------------------------------gtaagt-tctggtttttcaacctaggtttatgtggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccagg-tttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
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----------------------------------gtg-agttttagtattacgccaatcttttatttattcttgatgagcaattcttatggtttggaa----tctttttatattgggctattggcttatatatccgattctctttc----cagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATC
upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcat-tgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
||| ||| | || | | | ||||| | | ||| | ||||| || | | || | || || | ||| ||| | | ||||| || ||| | || || ||| | | || || | ||||||||||| |||||||| ||||| || |||||||| ||||| || |||||||| ||||
-------------------------------------------atttgtgttaatattttctgtaatagaactttggttctgc--tgctgctgcta-ctgttcttct-------gtttgcctattaaacttaattgtgtacatacttctgcagATTGGCTATTTAGACTATTGTCGGAGGAGAGGTTTTAGTAGTTGTTACATTTGGGCTTGCCCACCATTAAAGGGTGAGGATTATATTTTATATTGTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
gtctaat putative branch site (score: 3)
ttctcatt putative PPT
tttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA