Sequence
atgc intronic sequence ATGC exonic sequencegttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
Basic information
species | Glycine max |
transcript | GLYMA19G29100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
||||| ||| || | | || || | ||| | || | | || || || | ||| | |||| ||| ||||||| ||||||||| | |||| ||| ||||||||||| |||||||||||| | ||| || |||||||||| |||||||||| |
------------------------------gtttgtttgttaattgttgaggtactaatc-tgtacagccaatctgtagtttcatacttacattcaaagtgtttct--acagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 8
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgat-taaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
|||| | | || || | | ||| | || | || || | |||| | | | | | || |||| ||| | | ||||| ||||||||||| |||| ||| || ||||||||||||||||| || | | |||| | || |||||||||| ||||||||||| |
----------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G403493_T01 (Zea mays), 3'ss of exon 15
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgat-taaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
|||| | | || || | | ||| | || | || || | |||| | | | | | || |||| ||| | | ||||| ||||||||||| |||| ||| || ||||||||||||||||| || | | |||| || |||||||||| ||||||||||| |
----------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G03790.3 (Arabidopsis thaliana), 3'ss of exon 7
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
| | || |||| || | || | | ||| | | | | || |||| || ||| ||| ||| | || ||||| || | || ||| | | | |||||||| ||||| || || |||||| | | || ||||| ||||||||| |||||||||||||||||||
---------gttggattcaaccttctttttttat-cttaaaaaaacatataactcaatatgtctcgcatagtaata---accaaaatttggtt--aatcctgattcctgcagTTGCATTCGCTGCACGGTAAAACAGTTGTGAGCATTTCAGCGGGTAAATACTGGGCATCTGCTGTTACTAGTACAGGTGAAGTTTACATGTGGGATGGGA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0032g00280.t01 (Vitis vinifera), 3'ss of exon 8
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
|| | | |||| || | || ||| ||| || | ||||| ||| ||| | | | | |||| | | | |||| || ||||| || |||| ||||| | | | ||||| || || ||||||||||||| ||| ||||| |||||||||||||||||||| |||||||||||||
---gttttgcttgagtgaacttggtgtgccttttgaatttccatttgtcccaagtgaaacaggtttcttagttttcatctctgctcctttgcctct-tctggttttatgtagGTATATTCTCTGTGTGGAAGAACTGTATCCAGCATTTCTGCAGGAAAGTACTGGATTGCCGCAGTCACAGCTACAGGTGATGTTTATATGTGGGATGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
ttttaat putative branch site (score: 3)
cttccccccgttttgt CT-rich tract
ttttgttttaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG