Sequence
atgc intronic sequence ATGC exonic sequence...agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA13G42600.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
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--------gtaagttttgatctgaaattat-tatcttactacct----gtagttggttaacatcc--tcaccttaaaaagattatgaactcttttt--agGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatct-tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
|| |||| | ||| | | |||||| ||| | ||| | | || | || ||| || | ||| || || || || |||||||||||||||||||| ||||| || || || ||||||||||||||||| || || || |||||||||||||| | || | ||
---gtacgctgaatctgaacctac-tatctttacatt----tttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatct-tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
|| || | | | | ||| | |||| ||| | | | || |||| || || ||| || | | | || ||| | ||||||||||||||||||||||| ||||| || || || ||||||||||||||||| || ||||| || |||||||| || | || || ||
--------gtatgctaaatctgaaattactat-ctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
----agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
| || ||| || | ||| | | | || || || | | || | || | | || | | || || ||||||||| |||||| ||||||| ||||||||||||||||| ||||| || |||||||||||||||||||| ||||| || || || ||||||||||||| |||||||||
tatattttgcctgtggacggtagttt---ctttttctcgttgtt-ttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctaga--tgaaactgattttttgccattaaaatcttgttt----tgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
| | || | | | ||| | ||| ||| | | || || |||| || ||| || ||| ||| | ||| ||||| ||||| || |||||||| |||||||| || ||||| |||||||| |||||||||||||| || ||||| || || || |||||||| |||| | ||
---ttctcttgtattctcgtttcttc---tattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
--agatcccggtgaacttttttttacacagatatac--attaccatttctgtgcatttcctctagatgaa-actgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
| | || || | | || | | || | || || | | | ||| | ||||| | ||| || | | ||||| || || || ||||| || |||||||| || ||||| ||||| || || || |||||||| |||||||| ||||| ||||||||||| ||| | ||
ttcttttacattggaccacatctagaactaccacattaatcagaatgtcaggacttagccttggtttctgcactgacctattg--gttga---ttcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA
upper sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S255_47V6.1 (Physcomitrella patens), 3'ss of exon 6
----agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
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tgtttctttgcaccggattacctccaaaatggccatat-ttgtcactattaggatcgtgccttggttt---ctgcactgacaaaatattggatctaaactgcagATATGTGGCTCCTGAATACGCAATGACAGGACATTTGCTTGTGAAGAGTGACGTTTATAGTTATGGAGTGGTACTGCTCGAGCTCCTCTCGGGGCGTAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151397023|gb|EV266896.1|EV266896EST: CTGAACGAGGGAAACAAGCACATCTCAACACATGTTATTGGAACATTTGG CTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGA
genomic: CTGAACGAGGGAAACAAGCACATCTCAACACATGTTATTGGAACATTTGGgtaaaaatcc ... tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGA
EST:
gi|22524716|gb|BU083527.1|BU083527EST: CTGAACGAGGGAAACAAGCACATCTCAACACATGTTATTGGAACATTTGG CTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGA
genomic: CTGAACGAGGGAAACAAGCACATCTCAACACATGTTATTGGAACATTTGGgtaaaaatcc ... tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
aactgat putative branch site (score: 3)
tcttgtttt putative PPT
attaaaatcttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - ccatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgcc