Sequence
atgc intronic sequence ATGC exonic sequence...cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
Basic information
species | Glycine max |
transcript | GLYMA10G04700.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctac--ctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
|||| | ||| || ||| | | | ||| | | || ||| | || | || |||| | || || | | ||| |||||||| ||||||||||||||||| |||||| | || ||||| || ||||| || |||| ||| ||||| |||| || ||| | |||| || ||
ttcgtgctatcacaataat-tgttttcctacac-tttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
upper sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
cccgtggcttataaatcatgtgtg-attaaaatcattttttgatgccattgtaaattcctagc-cttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
| | || | | |||| || ||| | | || | || | || | ||| || || || | | || | |||||||||||||||| || |||||||||||||| || ||| |||| || ||||||||||| || |||| ||| || ||| ||||||||||||| | || ||||||
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgttta--tttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
upper sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
--cccgtggcttataaat-catgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
| | || || | | | | | | || | || || ||| | || || | | | | | | ||| || || | | | ||||||||||| ||||| ||||| ||||||||||| ||| |||| || || ||||||||||| |||| || || ||||| || ||||| || | || | |||
ttctcttgtattctcgtttcttctattttttagat-atctttggctggaccgctagcgttgttac--ttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctacctattcaattt---tgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
| | | | | ||| || | ||| || | |||||| | || || | ||| | | | || || | || ||||||||||| ||||| || || || |||||||| |||||||| || || |||||||||||||||| ||| || ||||| || ||||| || | || |||||
-ctttcaccttcacatc-tgaatatttaggat-gtattttgaccagactggtaaggttgtgtcttgattattgacttacggtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAA
upper sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S255_47V6.1 (Physcomitrella patens), 3'ss of exon 6
cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctacctattcaattt----tgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
|| ||| | | | | | ||| | || || | | | | ||||| || ||| | | | |||| || | ||||| ||||| || || ||||| ||||||||||| ||||| || || || ||||| |||||||||| ||| || || ||||| ||||| || | || | |||
--tgtttctt-tgcaccggattacctccaaaatggccatatttgtcactattaggatcgtgcctt-ggtttctgcactgacaaaatattggatctaaactgcagATATGTGGCTCCTGAATACGCAATGACAGGACATTTGCTTGTGAAGAGTGACGTTTATAGTTATGGAGTGGTACTGCTCGAGCTCCTCTCGGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgtaaattcctagccttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
tattcaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccgtggcttataaatcatgtgtgattaaaatcattttttgatgccattgtaaattcctagccttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
cccgtgg
- - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcca