RetrogeneDB ID: retro_zmay_3

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 7:39580163..39581666(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AC194457.3_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G160069
• Aliases: None
• Description: None

Sequence

>retro_zmay_3
ATGGCAGTGGCCGGGGCAATTGTTGGCGCTGGCGCAGGCGGTTGGATGAATGACCGGTTCGGGCGGCGACCGTCGATCCT
CATCGCTGACCTGCTCTTCCTGGCTGGCTCTATCGTCATGGCTTTTGCGCCTACGCCCGCGGTCATCATCGTGGGCAGAG
TCCTGGTCGGCCTTGGCGTCGGGATGGCCTCCATGACGTCGCCGCTCTACATCTCCGAGGCGTCGCCGGCGAGGATCCGG
GGCGCGCTGGTCAGCACCAATGGGTTGCTCATCACGGCGGGGCAGTTCCTCTCCTACCTCATAAACCTGGCCTTCACCAA
GGTGAGCGGGACGTGGCGATGGATGCTCGGGGTGGCCGGCCTACCAGCGCTCCTCCAGTTCGTGCTCATGCTGGCGCTGC
CGGAGTCACCGCGGTGGCTCTACAGGAAGGACCGAAAAAGGGAGGCCGAGGAGATCATGCGCAAGGTGTACCCGCCGGAG
GAGGTTGAGGGGGAGATTGAGGCGCTGCGTACGTCGGTGGAGGACGACATGGCCCAGGAACGGTCCCTCGGCGGCGCGGG
GCTCGCCGGCACACTCAGGAAGGCGTTCGGCAGCGTGGTGGTTCGGCGCGGCCTCACTGCGGGCGTGCTTTGCCAGGTGG
CGCAGCAGTTCGTCGGCATCAACACCGTCATGTACTACAGCCCGACCATCGTGCAGCTCGCCGGGTTCGCGTCCAACAGC
ACGGCGATGGCGCTGTCGCTCGTCACCTCGGGACTCAACGCCGCCGGGTCCTTGGTGAGCATGTTCTTCGTCGACAAGGC
GGGACGGCGGAGGCTGATGCTGCTCAGCCTCATGGGCGTCGTCGTGTGTCTCGGTATGCTGAGCGGGGTCTTCTTCGCGG
TGGACAGCCATGCGCCGGACGTCAGTCTGGCCGGGACAGCGCTCTTCGGCGCCAACGGCACGTGCCCAGAGTTTGACCTC
GCCGCCGTGGCCGGGGTGGAGTGGACCTGCGCCCAGTGCATCAAGGCTCCCTCAGGCTGTGGCTTCTGCGCGGACACCGA
AAAGCTCCTGCCCGGCGCCTGCCTTAGGACGTCGGACGCGTCGCGGCGCGCGTGTCGGGCGGGGCGGCGCGAGTGGTACA
TGCGGGGTTGCCCGAGCTCATTTGGCTGGCTGGCGCTGGTGGCGCTGGGCGCGTACATCGTGTCCTACTCCCCGGGCATG
GGCAGCGTGCCGTGGCTCATCAACTCGGAGGTGTACCCACTCCGGTTCCGGGGCGTCTGCGGCGGCATCGCGGCGGTGGC
CAACTGGACGTCCAACCTGCTGGTGACGCAGACGTTTCTCAGCCTCACACAGGCGCTGGGGACAGCGGGCACGTTCCTGC
TCTTTTGTGGTGTGTCGGCGATGGCGTTCCTGCTCATATTCCTTCTGGTGCCGGAGACTAAGGGGATGCACTTCGAGGAG
GTAGAGCAAATGCTAGGGAGCAAGGACTACAAGGCCTGGAAGAAGTTCAATTCCAAGGCCTAA

Alignment

ORF - retro_zmay_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.32 %
• Parental protein coverage: 52.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVAGAIVGAAFGGWMNDKFGRRPSIILADALFFGGAVIMAFSPTPRVIIVGRVFVGLGVGMASMTAPLY
          MAVAGAIVGA..GGWMND.FGRRPSI..AD.LF..G...MAF.PTP.VIIVGRV.VGLGVGMASMT.PLY
Retrocopy MAVAGAIVGAGAGGWMNDRFGRRPSILIADLLFLAGSIVMAFAPTPAVIIVGRVLVGLGVGMASMTSPLY

Parental  ISEASPARIRGALVSTNGLLITGGQFLAYLINLAFTKVPGTWRWMLGIAGVPALVQFVLMLMLPESPRWL
          ISEASPARIRGALVSTNGLLIT.GQFL.YLINLAFTKV.GTWRWMLG.AG.PAL.QFVLML.LPESPRWL
Retrocopy ISEASPARIRGALVSTNGLLITAGQFLSYLINLAFTKVSGTWRWMLGVAGLPALLQFVLMLALPESPRWL

Parental  YRKGRKEEAAAILHKIYPANEVEEEIDSMRRSVEEEVLLEGSIGESGFMGKLRKAMGSKVVRRGLTAGVI
          YRK.RK.EA..I..K.YP..EVE.EI...R.SVE.....E.S.G..G..G.LRKA.GS.VVRRGLTAGV.
Retrocopy YRKDRKREAEEIMRKVYPPEEVEGEIEALRTSVEDDMAQERSLGGAGLAGTLRKAFGSVVVRRGLTAGVL

Parental  VQVAQQFVGINTVMYYSPTIVQLAGYASNNTAMALSLITSGLNAIGSIVSMFFVDRAGRRRLMLISLVGI
          .QVAQQFVGINTVMYYSPTIVQLAG.ASN.TAMALSL.TSGLNA.GS.VSMFFVD.AGRRRLML.SL.G.
Retrocopy CQVAQQFVGINTVMYYSPTIVQLAGFASNSTAMALSLVTSGLNAAGSLVSMFFVDKAGRRRLMLLSLMGV

Parental  VVWLAVLGGTFLGAAHHAPPVSDLETRL
          VV.L..L.G.F.....HAP.VS...T.L
Retrocopy VVCLGMLSGVFFAVDSHAPDVSLAGTAL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Zea mays was not studied using RNA-Seq expression data.

ChIP-Seq

Zea mays was not studied using ChIP-Seq data.

EST

Zea mays was not studied using EST data.

TSS

Zea mays was not studied using FANTOM5 data.

Lab

retro_zmay_3 was not experimentally validated.

Homology

Retrocopy orthology:

Zea mays does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G160069	1 retrocopy	retro_zmay_3 ,