Sequence
atgc intronic sequence ATGC exonic sequencetcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
Basic information
species | Glycine max |
transcript | GLYMA18G04730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 2
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtt-tctttcttccaa----cagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
||| | ||| || ||||| || | ||||||| | | ||| || ||| || || || | |||||| || ||| || || |||||||| | ||||||||||| ||||| || || || |||||||||||||| ||||| || || |||||||||||||| || |||||| ||
--------------------------------------------------------------------------------gtggtagct-tatcat--cttatatcaaaacaaaatattgtctggctgcttcttcaagctacccttggccggtttgtaactttgtatttcttgaaaaatgcagGTGCGTCAGATTTGCTAGTGAGGTTGCTGGTGTTCAAGACCTGGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTGGAGAAACTTATG-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 2
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattact-ttaatctgagtgcc-tgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
|| | | | | || || | ||||| ||| | | | | ||| | | | |||| || ||| | ||| ||||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||||||||| ||||| || || ||||||||||||||||| |||||| ||
------------------------------------------------------------------------------tttttaatttgttgtcat--ctcgtgctgtagaacaattgttctcgcaacttgtgcaagttctgtacattggctgatatgtgatgctatttttaaattgcagATGTGTCAGGTTTGCTACTGAGGTTGCTGGTGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 2
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
| | | ||||| | ||||| | | | | || | | | | | || || ||| |||| | | || || || || |||| ||| ||||| || ||||| || ||||||||||| ||||| || ||||| |||||||||||||| ||||| || || ||||||||||||||||| |||||| ||
--------------------------------------------------------------------tcttacattgcattg-acatcatgtgctaaatggttctctctacttgtgcaagct-ctgtatcctgg----ctgatatg----tgatgctattttattttcaaattgcagGTGTGTAAGGTTTGCTACTGAGGTTGCTGGAGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
||| ||| || | ||| || | | ||| ||| || || | | ||| || ||| ||| || | || | || | ||| || ||||| ||||||| | || ||||||||||||||||||||||| || |||||||||| ||||||||||| |||||||| ||||||||||| ||| ||
------------------------------------------------------------gttactaa------tatagtttgcttatagtgtgatgttttagtt------aatgtgatagatacgctatcctg-----ttgattaggttttgtatgtataatgttttt-----gtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgact-tatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
| | ||| || || | | ||| ||||| | | | | | | | | ||| | | | | | || || | | ||| |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| || ||||| || |||||||| ||||| || ||||||||||||||| ||
-----------------------------------------------------------------------tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgcatcattct-------ttacaagcttttgatgtga-acatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG-Mapped 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|254341815|gb|GR852952.1|GR852952EST: TTGGACCTCTGGTGAAGACTGTGATGACTCGGTGCATTCAATGTACAAGA TGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTA
genomic: TTGGACCTCTGGTGAAGACTGTGATGACTCGGTGCATTCAATGTACAAGGtcaatattgg ... ttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
ctttaat putative branch site (score: 4)
tgtttctttcttcc putative PPT
aatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgacttatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT