Sequence
atgc intronic sequence ATGC exonic sequencegttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
Basic information
species | Glycine max |
transcript | GLYMA10G37210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 4
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
|| | | || || | ||| ||| | ||||| || | || | | | |||| ||| |||||||||||||| || || ||||| ||||| || ||||||||| |||||| ||||||||||| |||||||| ||||| || |||||| ||||| |
----------------------------------------------------------------------------gtaatagtcaacattcatttcactgaatattataaacactcttgtttc----------attctcattttctgaacttgc---agACAAGGATTGGGATGATATTAAGTTTGGTGTGGAGAATCAAGTTGACTACTATGCCGTTTCTTTTGTCAAAGATGCTCAAGTTGTGCATGAATTGAAGGA
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
||| | || ||| ||| | || | | | | | | | ||| || | | | |||||| ||||| ||||| ||||| || ||||| |||||||| ||||||| | |||||||||||| ||||| |||||||| ||||| || || ||||| ||| |
-------------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatcctt--------gtttcatacacgtttcaaatg--tacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactg-acaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
| ||| | | ||| || | || || |||| ||| | || || || | | | || | ||| | || || | | || | | | | || |||| |||||||||| ||||| || || |||||||||||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||| || || || |||||||
------------------------gttcgaattttctgtttaccctctttttcactttttcttgttgctttg------gttgaagtgttgcatatttaagtctga---aagatctta-----ctctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 4
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactga-caactgggtgagggttaaggtt--ttgttggtttcccaaggacatataata-tttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
|||| | || | | | | ||| | | || |||| ||| | |||| | |||| |||||||||| |||| ||||| |||||||| ||||| ||||| || || || ||||| ||||| ||||| || || ||||||||||||||| ||||||| |||||| |||||||
-------------------------------------------------------------------------------gttggacatggaatgagtccccaatgtttatagcaaatgctttgttttgcaattcaaaataacaatttgctttgatttgctgcagAAAAGGACTGGGATGATATCAAGTTTGGTGTTGACAATAAAGTGGACTTTTATGCAGTCTCCTTTGTTAAAGATGCAAAAGTAGTCCATGAATTGAAGAA
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
| | |||| | | |||| | || | | ||||||| | || | | | ||||| | |||| ||| | || || | || || || | | | ||| ||| || | || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| ||||| | || ||||| || ||||| || || || |||||||| |||
-----------gtatgccattttt-ttgtgatcgaataaggccatatcgat--atttcttttgt-tgtcatatcttttatttag--actg---tctgatttagacactccgtcgcttgctcttgtcacctacttttg-tttttctgtggaat--ctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
upper sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
| || ||| ||| || | |||| | || | | || || |||| || | || | | ||| || || || ||| || | || |||||||||||||||| ||||| ||||||||||| || || |||||||| ||||| || | || ||||| || || || || || || ||||| || ||
---------------------------------aatttcattagtgtgcaatcactatctctagagatctatagaaattttat----ctgaacac------ggactttggataccattgtgtttcc---------------ttctgtggagt--ctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATCMapped 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|207776151|gb|GD749948.1|GD749948EST: GAGACATTTGAATGTTAGAGGAAAAAGTGCAACACTTCCTTCCATCACTG AGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
genomic: GAGACATTTGAATGTTAGAGGAAAAAGTGCAACACTTCCTTCCATCACTGgttagattcc ... tttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
EST:
gi|151410647|gb|EV280462.1|EV280462EST: GAGACATTTGAATGTTAGAGGAAAAAGTGGAACACTTCCTTCCATCACTG AGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
genomic: GAGACATTTGAATGTTAGAGGAAAAAGTGCAACACTTCCTTCCATCACTGgttagattcc ... tttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
tgttgat putative branch site (score: 4)
atataatatttgtgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA