Sequence
atgc intronic sequence ATGC exonic sequence...acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
Basic information
species | Glycine max |
transcript | GLYMA10G30020.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctcct---taattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
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----------------------gttagt-taagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 6
-----------acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
||| || | | | |||| | || ||| || ||| || ||| | | | ||| || | |||| | |||||||| || || |||||||| ||| || |||||||| | ||||| ||| |||| |||||||||||||||
gtttgtacaacacaccacattatgtggttgatatttg---tatgatcaatcaccagacattttataataattctct------aatcca--tgaattataccttcaatccagGCATTCCACTGATCGTGAAGTTTCTATTATGATGCTCATGGCTTACTTGTCTTACATGCTTGCTGAA
upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
acaaggttttttag-acccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
|| ||| | | ||| | || || | ||| || |||| | ||| ||| | || ||| |||||| || || || ||||||||||| ||||||||| | ||||| ||||| ||||||||||| || ||
gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcga----gaacatcaagtattaacttggctgcttgctgtcct----gatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 7
acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttga-aacaatctttttta---ctgaggccaa--acaaaatt-ctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
||| | | | ||| || | || || || || |||| | | | | | || ||| |||| || || |||||||||||||| ||||| |||||||| ||||||||| | ||||||||||| |||||||| |||||||||
-------tttatgataaaacctcagatcatgtaggaatacatataataatacgagaataatcatactaaagacaaaatacacttacagaatttctgacaaaatccagGCACTCTACTGATCGGGAGGTTGCCCTTATGATGCTTATGGCATACCTTTCCTACATACTTGCTGAAMapped 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|21601836|gb|BQ612167.1|BQ612167EST: ACAGGTCTACTTAGTGCTTACATTATTAAAAAGCTGTACATTGGCAG GCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTC
genomic: ACAGGTCTACTTAGTGCTTACATTATTAAAAAGCTGTACATTGGCAGgtaccttctt ... ttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTC
EST:
gi|254323350|gb|GR835851.1|GR835851EST: ACAGGTCTACTTAGTGCTTACATTATTAAAAAGCTGTACATTGGCAG GCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTC
genomic: ACAGGTCTACTTAGTGCTTACATTATTAAAAAGCTGTACATTGGCAGgtaccttctt ... ttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
ccttaat putative branch site (score: 4)
ttctccttaattcc CT-rich tract
aaacaatctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
- - - - - - -gacccgc
- - - - - - - - - - - - -ggtatga
- - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaca