Sequence
atgc intronic sequence ATGC exonic sequencegtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaat-ttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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--------------------------gtttgccaccttgaatct-cacttgttctgcttttactgtgtcaattggtaccttacagtcttggtgtttgtatcagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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----gtatgtttgctcttgtaggctt--tcattgtgttgtatatatgcc-atttacagctaatcaaattcttatt--tggcctattgttggtcaaccattagGGCTTGGGGAAGCATGACATCATCTGCATTGAGGATCTTGTCCACGAGATCATGACTGTCGGTCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCCT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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----------------------gtattgtttat-tttacaattcttccttacagattttaattaattcgctacatgcttcttac---ttgcttggatgacagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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gtccgtgtggtctattctgtagtcc---tctgtaaacacttccattgcttgtttgttct--attacttagtttttttccctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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------------------gtattgttaatttaca-attctgtat-tacaaatttgaatt----aattcactacatgcttctgac---ttgcttggatgacagGCGCTGGGCAAATATGGAATCATTTCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGGCCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------------------------gtttgtaaacttggaactg-tacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtaaacttggaactgtacatctggttcctgtgttctg--tttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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----------------gtttttatgtcattc-tgtatcttggttttctatgagcgattgtttg-----ctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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----------------gtttttatgtcattc-tgtatcttggtttt--ctatgagcgattgtttgctt-tatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtaaacttggaactgtacatctggttcctgtgttctgt-ttatatttgtttatatttgacaatttac---atgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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---------------------------gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
|||||| || | | || || || | ||||| | ||| || | | || | || | |||| || | | || ||| |||| |||| |||| |||||| ||| | || ||||| | || ||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||
gtttgt-----tgtaggt-taaataacatttatatgttcgatgtat---tgctataaactggcttttca-atgac-attttggtatgttattg------cagGCTTTGGGCAAGTTTGGAATCATTTGCATTGAAGATCTCATCCATGAGATTATGACTGTTGGGCCACACTTCAAGGAGGCAAACAACTTCCTGTGGCCAT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ20182 (Selaginella moellendorffii), 3'ss of exon 5
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgtt-gttctatc--agGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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-----------------------------------------gtaagatccttttcta--cgatgacttctctagttctcatcgtttcttatttgttctttctcagAGCTTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTCGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTT
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 5
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttaca-tgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
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------------------------------------------gtacgatccttt-tctacgatgacttctagttctcatcgtttcttatttgttctttctcagAGCCTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTTGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
atttgac putative branch site (score: 4)
ccttttgttgttct putative PPT
ttatatttgacaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG