Sequence
atgc intronic sequence ATGC exonic sequencegtaagagacacataagcacatttgatttctggaatatgtaaattatgttacatatggtgtagttgtggttggaaagttaacattcttgatgctcttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
Basic information
species | Glycine max |
transcript | GLYMA02G29830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G29830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g39630.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------gtaagagacacataagcacatttgatttctggaatatgtaaattatgttacatatggtgtagttgtggttggaaagttaacattcttgatgctc------------ttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
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gtactgatgagtactacacctctctctctctctctctctctctctctcttccccaataggcaatagaacagtgtttggttagcaaatagtagcagtagtagcagcaaatctgcaaatgtgcagtacaaggaccactccaaaattaacctgtccgaaacctgaaacgtttccgttttcctgcagCAAACCAACACTGCTGACATGCTGGATTTGGCTGTTGACTACATCAAGGATCTTCAGAAGCAGGTCAAG
upper sequence: GLYMA02G29830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G417597_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------gtaaga-gacacataa-----gcacat-ttgatttctggaatatgtaaattatgttacatatggtgtagttgtggttggaaagttaacattcttgatgctcttaattg------gcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
|| | | | ||| | || || | | | ||| | | | | | || | || | | || || ||| | | | || ||| ||||||||||||||| || |||||| |||| ||||||| || ||||| || ||||||||||| || |||||
gtaaccaaacccagcccaaaccccaagaaagatggatagaacagtgaaacgtcacgccattcccgctcacctccactcctgattggtactaccagtaccaga-atagaacagcgagagattgatagataaactgacgaccggttttcgttgatggctgcagCAAACCAACACTGCCGACATGCTGGATCTGGCTGTGGACTACATCAAGGATCTTCAGAAGCAGGTCAAG
upper sequence: GLYMA02G29830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G153454_T01 (Zea mays), 3'ss of exon 5
gtaagagacac---ataagcacatttgatttctggaatatgtaaattatgttacatatggtgtagtt-gtggttggaaagttaacattcttgatgctcttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
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gtactccacattctgtatgtagcctacacttccattcc-tatgggatctgaggaggaccacccaccccataattgaattgtctgcaacctacacttgtatttcctgcagCAAACCAACACATCTGACATGCTGGATTTGGCTGTCGACTACATCAAGGATCTCCAGAAGCAGGTTAAG
upper sequence: GLYMA02G29830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07810.t01 (Vitis vinifera), 3'ss of exon 4
gtaagagacacataagcacatttgatttctggaatatgtaaattatgttacatatggtgtagttgtggttggaaagttaacattcttgatgctcttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
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gtagaatttctatgaa---attttcctctctggttggataaattttttca---atgtttcaattcaacttctaa--ttaatatctgtga-attcttc-ttggcagCAAACCAACACTGCAGACATGTTAGATTTGGCCGTGGAATACATTAAGGACCTTCAGAAACAGTACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatggtgtagttgtggttggaaagttaacattcttgatgctcttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
tcttaat putative branch site (score: 3)
tgctctt CT-rich tract
aaagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagacacataagcacatttgatttctggaatatgtaaattatgttacatatggtgtagttgtggttggaaagttaacattcttgatgctcttaattggcagCAAACCAACACAGCAGACATGTTGGACTTGGCTGTTGAATACATTAAAGATCTTCAGAAACAATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT