Sequence
atgc intronic sequence ATGC exonic sequence...tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
Basic information
| species | Glycine max |
| transcript | GLYMA20G30100.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggtt-ccttatagaggcttctaaatcacccctt------gaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
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------ccacattctgcagaattttac-gaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
--tgtttc-tggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagaggcttctaaatcaccccttga-acagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
||| | || | | | | ||| ||| | | | |||| | || |||| | || | | || ||| | | | || | |||||| ||| | |||||||| |||||| | |||||||||||||| || || || ||||||||||| | ||| ||||| || ||||||||| || || || |
gaagttgcatgatagcatctaggatttcattaatg-agttatttatgtaccacttttgattttct---tttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttcctt-atagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
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tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatc-ttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
-tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttcct-tatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
| || | ||| ||| | || | || || | || | ||||| ||| | || | || | || || |||| ||| | ||||||||||||||||| |||||||| ||||| || || |||||||| ||||| | ||| ||||| || |||||||||| || ||| | |
tagaatcacattcttttctggatgg-agggagtacatagttacttttccccatgcatc-ttgtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 4
---tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggtt--ccttatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
||| | || || ||| ||| | || || | | | || || || | | |||||| | || | ||| | |||| || | || ||||||||||| | || ||||| ||||| || ||||||||||||||||| | ||||||||| || ||||||||| || || || |
gagagttcacaacagcttgtcacatatcattaatagggttatggatgcattattttcatttttaggcatgaacttataca-----ttatgtttgcccaaaattagGTTGAAGATAAACTTTACATATATTTGGAATATGTTTCTGGTGGATCCATACATAAACTTCTACAAGAATATGGACAGCTTGGTGAACCAGCAATACGCA
upper sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagagg-----cttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
| || || | || | | || | | || || | || | || | || || || | | || ||| | || ||||||||| | | |||| ||||| |||||| | |||||||||||||| |||||||| |||||||||||| ||||||||| ||| |||||||||||| |||||||
----tttgcaatattgttgcatcatgtgcaa-tattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acggtatttgttattgtggttccttatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
ttctaaa putative branch site (score: 2)
tcacccctt CT-rich tract
atttgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
- - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcacc
