RetrogeneDB ID: retro_ogar_3376

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873808.1:269989..271546(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC30A9
• Ensembl ID: ENSOGAG00000000501
• Aliases: None
• Description: solute carrier family 30 (zinc transporter), member 9 [Source:HGNC Symbol;Acc:1329]

Sequence

>retro_ogar_3376
ATGTTACCGGGCTTGGCCGCCGCCGCTGCGACCCATAGATGTAGCTGGTCCTCACTGTGCCGGCTCCGTCTGCGCTGCAG
GGCGGCGGCCCACGGCTCCAGCGACCGCCAGGGATGGCAGAATTTGGTGACATTTGGAAGCTTTTCAAACATGGTTTCAT
GTAGTCCTTCATATGTTTGTATACTCAGTCAAGTAAAGTCGTATTCCACGAATATTCAGAAAGAAGGACAAGGATCACAG
TCTCTCAGAGTGGAAAAAGTATCATCTCTTGATGAAACAGCAGAAAATATAGGTGCAGAACTCAAAGCTCCACTTAAGCA
AGACCCTCTCCAAGTAAGAGTTAAAGCAGTTCTTAAGAAAAGGGAGTATGGATCAAAGTACGCTCAGAATAATTTCATTA
CTGGAGTCAGAGCAATGAATGAGTTCTGCCTTAAATCCAGTGATCTAGACCAACTTCGAAAAATTAGACGACGAAGTCCC
CATGAAGATACTGAGTCCTTTACTGTATACTTGAGATCAGATGTGGAAGCAAAATCTTTGGAAGTCTGGGGAAGCCCTGA
AGCTCTTGCCAGAGAAAAGAAACTGCGTAAGGAAGCAGAGATAGAATACAGAGAACGGCTGTTTAGAAATCAAAAAATAT
TAAGAGAATATAGAGATTTCTTGGGAAACACCAAGCCACGCTCCAGAGCCGCATCAGTGTTCTTTAAAGGACCAGGAAAA
GTGGTGATGGTTGCCATTTGCATCAATGGGTTAAACTGTTTCTTTAAATTTCTTGCCTGGATTTATACGGGTTCAGCAAG
TATGTTCTCAGAAGCTATACACTCACTGTCTGATACTTGTAATCAGGGTTTACTAGCATTGGGCATCAGTAAGTCTATTC
AAACACCAGATCCTTCTCACCCTTATGGATTTTCAAATATGCGCTATATTTCTTCGCTATTTAGTGGTGTTGGTATTTTC
ATGATGGGTGCAGGACTATCGTGGTACCATGGAGTCATGGGATTGCTTCATCCTCAACCAATAGAATCCCTTCTATGGGC
ATATTGTATTTTAGCAGGATCATTGGTATCTGAAGGAGCCACACTTCTTGTTGCTATAAATGAACTTCGTAGGAGTGCTC
GGGCCAAAGGAATGTCATTTTACAGATATGTAATGGAAAGTCGTGATCCTAGTACAAATGTGATATTATTGGAAGATACT
GCAGCAGTATTGGGAGTGATAATAGCAGCTTCTTGTATGGGCCTTACTTCTATAACAGGCAATCCGCTGTATGACAGCCT
AGGTTCTCTGGGTGTGGGCACCTTATTAGGTGTGGTATCAGCTTTCCTCATCTACACTAACACAGAAGCGCTCTTAGGGC
GATCCATCCAGCCAGAGCAAGTCCAGCGGCTTACTGAACTCCTGGAGAATGACCCATCAGTAAGGGCAGTTCATGATGTT
AAAGCCACAGATCTGGGATTAGGTAAAGTCAGATTTAAGGCAGAAGTAGATTTCGATGGACGAGTTGTTACGAGATCATA
TTTGGAGAAACAAGATTTTGACCAAATGCTACAGAAA

Alignment

ORF - retro_ogar_3376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.42 %
• Parental protein coverage: 91.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLPGLAAAAATHRCSWSSLCRLRLRCRAAAHGSSDRQGWQNLVTFGSFSNMVSCSPSYVCILSQVKSYST
          MLPGLAAAAATHRCSWSSLCRLRLRCRAAAHGSSDRQGWQNLVTFGSFSNMVSCSPSYVCILSQVKSYST
Retrocopy MLPGLAAAAATHRCSWSSLCRLRLRCRAAAHGSSDRQGWQNLVTFGSFSNMVSCSPSYVCILSQVKSYST

Parental  NIQKEGQGSQSLRVEKVSSLDETAENIGAELKAPLKQDPLQVRVKAVLKKREYGSKYTQNNFITGVRAMN
          NIQKEGQGSQSLRVEKVSSLDETAENIGAELKAPLKQDPLQVRVKAVLKKREYGSKY.QNNFITGVRAMN
Retrocopy NIQKEGQGSQSLRVEKVSSLDETAENIGAELKAPLKQDPLQVRVKAVLKKREYGSKYAQNNFITGVRAMN

Parental  EFCLKSSDLDQLRKIRRRSPHEDTESFTVYLRSDVEAKSLEVWGSPEALAREKKLRKEAEIEYRERLFRN
          EFCLKSSDLDQLRKIRRRSPHEDTESFTVYLRSDVEAKSLEVWGSPEALAREKKLRKEAEIEYRERLFRN
Retrocopy EFCLKSSDLDQLRKIRRRSPHEDTESFTVYLRSDVEAKSLEVWGSPEALAREKKLRKEAEIEYRERLFRN

Parental  QKILREYRDFLGNTKPRSRAASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTC
          QKILREYRDFLGNTKPRSRAASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTC
Retrocopy QKILREYRDFLGNTKPRSRAASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTC

Parental  NQGLLALGISKSIQTPDPSHPYGFSNMRYISSLISGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCI
          NQGLLALGISKSIQTPDPSHPYGFSNMRYISSL.SGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCI
Retrocopy NQGLLALGISKSIQTPDPSHPYGFSNMRYISSLFSGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCI

Parental  LAGSLVSEGATLLVAINELRRSARAKGMSFYRYVMESRDPSTNVILLEDTAAVLGVIIAASCMGLTSITG
          LAGSLVSEGATLLVAINELRRSARAKGMSFYRYVMESRDPSTNVILLEDTAAVLGVIIAASCMGLTSITG
Retrocopy LAGSLVSEGATLLVAINELRRSARAKGMSFYRYVMESRDPSTNVILLEDTAAVLGVIIAASCMGLTSITG

Parental  NPLYDSLGSLGVGTLLGVVSAFLIYTNTEALLGRSIQPEQVQRLTELLENDPSVRAVHDVKATDLGLGKV
          NPLYDSLGSLGVGTLLGVVSAFLIYTNTEALLGRSIQPEQVQRLTELLENDPSVRAVHDVKATDLGLGKV
Retrocopy NPLYDSLGSLGVGTLLGVVSAFLIYTNTEALLGRSIQPEQVQRLTELLENDPSVRAVHDVKATDLGLGKV

Parental  RFKAEVDFDGRVVTRSYLEKQDFDQMLQE
          RFKAEVDFDGRVVTRSYLEKQDFDQMLQ.
Retrocopy RFKAEVDFDGRVVTRSYLEKQDFDQMLQK

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3376 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376 ,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658,