Sequence
atgc intronic sequence ATGC exonic sequence...tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
Basic information
species | Glycine max |
transcript | GLYMA16G30030.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaaactgccaaat--catccctt------aaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
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----ccacattct-gcagaattttacga-acttcacttttgcttgcact-cctgactcctctgtttactt-taaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 4
tggtttacatttttacttgtcat-cattat-attagatacttgtttacagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
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gagagttcacaacagcttgtcacatatcattaatagggttatggatgcattattttcatttttaggc-atgaacttatac-attatgtttgcccaaaattagGTTGAAGATAAACTTTACATATATTTGGAATATGTTTCTGGTGGATCCATACATAAACTTCTACAAGAATATGGACAGCTTGGTGAACCAGCAATACGCA
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
-tggtttacatttttacttgtcatcattatattagatacttg-tttacagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
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tagaatcacattcttttctgg-atggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatct-ccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
-tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaa-actgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
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tagaattgcattcttttttgg-acggaaggagtacatagttatttttcct-catgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
tggtttacatttttact-tgtcat-cattatattagatacttgtttacagtatttgtctt--ttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
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---tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacct-cccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
tcatccctt CT-rich tract
atagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
- - - - - - - -cttgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgccaa