Sequence
atgc intronic sequence ATGC exonic sequence...ctaatgattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttcttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
Basic information
species | Glycine max |
transcript | GLYMA05G36070.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 16
-ctaatgattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttc-ttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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agaattgattatatcttggaataaaat--tattaaatgaatgtcatgtttgatagtgttgtgatgcttggaattaacatctgcctacttcataaatctttagGTGACTGCAACTCCTGATCTTATGCTGGGCTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGCCAAAGGTTTC
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 14
-ctaatgattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttcttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
|| | |||| | || | || | | || | ||||||| | | | ||||||| ||| | |||| ||||| ||| | ||| | |||||||| ||| | |||||||| |||||||||||||| ||||| ||||| || || ||||||||| ||||||| || |
tacaagaaccagaactgcacttgtattatgaatttttatacaattatcagtctcatcacatcatggattgaggtatgctttctggttttc-catttgatagGTTGCTGCTACACCAGATTTAATGCTGGGTTATTTAGATTTCTTTCTTGGTGGGGATGAAAAAAGGCCTGACCTCCCCCCTCGTCTTCATCAAAGGTTGC
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G350818_T01 (Zea mays), 3'ss of exon 9
ctaatgattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttcttagtt---ggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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-tagtatcggaaagcataggttgcgttactcttgcaattgtttacaggtg-aattgtcttgtcatatataggattgatggtttctgatttccaaat-taatagGTAGCTGCTACTCCAGATTTAATGCTGGGTTATTTAGATTTCTTCCTTGGTGGGGATGAGAAAAGGACTGATCTTCCTCCTCGGCTTCATCAAAGGTTTC
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 6
ctaat-gattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttcttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
| || | | | | |||| || || | | || | | | | ||| ||| | || |||| ||| |||| ||||||| | ||||| ||||| || ||| | |||||||||||||| || ||||| ||||| |||||||| || ||||||||| |||||| ||||
ttgatcaactgtatactgtttatgctcattattgtttccgaagctggaatagtacctttcagcctgtcatttatttaatttctgcttttgcaatgtc-tagGTGACTGCAACCCCAGATCTAATGCTAGGGTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGTCAAAGGTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggggcagattctttgatggatttttttttcttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
ttttaac putative branch site (score: 2)
atttttttttcttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaatgattccaactaactgttgcttcttgtttgggggggggggggggggcagattctttgatggatttttttttcttagttggttttaacatgctacagGTAGCTGCAACATCTGATCTGATGCTGGGATATCTGGATTTCTTCCTTGGTGGGGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - -ccaacta
- - - - - - - - -ctgttgc
- - - - - - - - - - - - - - -gtttggg
- - - - - - - - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg