Sequence
atgc intronic sequence ATGC exonic sequencegtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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------------------gtgagggcaacattatagtat--tcatctgataccatgtatttccattaagtggttccccatg-atctccaac----------------acagtact---aatgtttctct------cttccgtcacagGGAGCGCTCCTCTCACTGCTGTGCAGCTATTGTGGGTCAATATGATCATGGATACACTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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-------------------------------------gtgagggcaaca--ttatag-tattcatctgatg---ctatgtatttccattaagtggttctccatgatctccaagac---agtactaatgttttgctcttccgtcacagGGAGCGCTCCTCTCACTGCTGTGCAGCTGTTGTGGGTTAATATGATCATGGATACATTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgc--tttgagtgctgtactactgtactg--ctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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--------------------------------------------------gtaata--catacagctagcttttcaagac-tatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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---------------------------------------------------gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccattt----------cttttg-gtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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-------------------------------------------------------gtaagtaaaatca--aacacatgcacaattttcaccaatgat-ttttgaataacagt---ttcagtaatg-attgttttgc-accttttcagGATCTGCGCCACTCACCGCAGTGCAACTGCTTTGGGTGAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCGACCGAACCTCCCAACGAAGGTTT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ18007 (Selaginella moellendorffii), 3'ss of exon 3
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
| | | | | || || | ||| | || || | || | | | || || | | | |||||| ||||| ||||| || ||||||||||||||||| || |||||||||||||| |||| ||||| ||||| || || ||||| || | || || |
--------------------------------------------------------------------------gtaagattctttact-ctttaagttcttgggtctca----tatgtgactttttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTGCTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
upper sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
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--------------------------------------------------------------------------gtaagattctttact-ctttaagttcttgggtctca-tatgtgacattttcttctcttgt--cgttg-atcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
gagtaac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT