Sequence
atgc intronic sequence ATGC exonic sequence...atttctctaatctcttggagattctcttagcttttattataatctaacactacagttggaaaatgatgtattgatacgcatttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g56960.1 (Oryza sativa), 3'ss of exon 3
-----atttctctaatctcttggagattctcttagcttttattataatctaacactacagttggaaaatgatgt-attgatacgcatttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------
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tgaccagctatttcctttcttgaaatcttgtactacaaaactaataatgcatagcttcacgattagcctgaccttataaatatgcacttccatga------tgcagGTTCTGCCATCACTGGACCTATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCAAGTGCAGCAAATGCGATCGTCTAATCGAAGCAGCCATTGAA
upper sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT3G04400.1 (Arabidopsis thaliana), 3'ss of exon 3
atttctctaatctcttggagattctcttagcttttattataatctaacactacagttggaaaatgatgta-ttgatacgcat-ttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------
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agaagtttgatatggggcaactcaaagccaatctcgtagtgataaatcagtagtatcatatttacttgtagctgatgagtctgttgtgtgat-gtaat-tagGATCTGCTATCACTGGACCAATCGGAAAGGAGTGTGCTGATCTGTGGCCAAGAATCGCAAGTGCTGCGAACGCCATCGTTTAAGCAAGCTTGAGATCTCT
upper sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S280_69V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------atttctctaatctcttggagattctcttagctt-ttat-tataatctaacactacagttggaa--aatgatgtattgatacgcatttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------
|| | | | ||| || | | | | | | || | | | | || | | || | |||| || ||||| | ||| || | |||||| ||||| |||||||| || || || |||||||| || ||| |||||||||||||||| || || || ||||| |||||||
gtacgcagatatttccctcaaatatctttgacgtcagattcgttttagcaaaagatccagttagcgaatgagaatgattggcagatatatgtcatcgtatgttgttcttatcggaatgttgtgcacgttatgacttttgggatgagcctactgatttactgataggttttttggcaacttt--tgcagGTTCTGCTATCACTGGTCCTATTGGGAAGGAGTGCGCCGATTTGTGGCCTAGGATTGCTAGTGCTGCCAATGCCATTGTCTGAGGGCAATAGTTGTAATA
upper sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S15_152V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------atttctctaatctcttggagattctctt----agcttttattataatctaacactacagttggaaaatga-tgtattgatacgcatttccatgacca-tgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------
|||| || | | ||| | || | | | || || || ||||| | || | | | | || || | || | | | |||||| ||||| |||||||| ||||| ||||| |||||||| || ||||||||||||||||||| || || ||||| ||||| |
gtaatctcacttacatctatttgattttaggaaatacattcagttggtctgttctgtgaaatctgtcttacagtagttacctacttgattttaaagattacagtcatatttttttgttcaaccactcttgtactcatgtgaagttgttgggactggagtttgatcaaaccaatgtttttggcaacttgtgcagGTTCTGCTATCACTGGTCCCATTGGAAAAGAGTGTGCCGACTTGTGGCCTAGGATTGCCAGTGCTGCTAATGCTATTGTATGAGTGCAATAGTTGCGCAT
upper sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------atttctctaatctcttggagattctcttagcttttattataa----tctaacactacagttggaaaatgat-----gtattgatacgcatt-tccatgaccatgatg--cagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------
||| | || ||||| | | | | || | || || | ||| | |||| | || | | || | ||| |||| ||||||||||||||||| ||||| |||||||| || || ||||||| |||||||| ||||| || || |||||||| |
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacactacagttggaaaatgatgtattgatacgcatttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG
aaaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttctctaatctcttggagattctcttagcttttattataatctaacactacagttggaaaatgatgtattgatacgcatttccatgaccatgatgcagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - -cactaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgta