RetrogeneDB ID: retro_mdom_861

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:234811375..234812994(-)
• Located in intron of: ENSMODG00000002436

Retrocopy information

• Ensembl ID: ENSMODG00000002445
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSMODG00000002356
• Aliases: None
• Description: chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618]

Sequence

>retro_mdom_861
ATGTCTTCCATGGGGACTCTGGAATTTGACGAATATGGCCGTCCTTTCCTCATCATCAAGGACCAAGAGCGCAAGTCTCA
TCTTATGGGACTGGAGGCACTCAAGTCTCACATAATGGCGGCTAAGGCTGTATCAAATACAATGAGAACATCACTTGGAC
CTAATGGGCTTGATAAAATGATGGTGGATAAGGATGGTGATGTGACTGTAACCAATGATGGTGCCACCATTTTAAGCATG
ATGGATGTAGATCATCAGATTGCTAAACTAATGGTTGAACTTTCCAAATCACAGGATGATGAGATTGGAGATGGGACTAC
AGGAGTAGTTGTTTTGGCTGGTGCTTTGTTGGAAGAAGCTGAACAACTGCTGGATCGTGGTATTCACCCAATCAGAATAG
CAGATGGTTATGAGCAGGCTGCTCGCATTGCCATTGAACATTTGGACAAAATCAGTGAAAGTTTTCCAGTTGATGTTGGA
AACACTGAACCCCTCATCCAGACTGCAAAAACAACTCTTGGTTCTAAAGTAGTTAACAGCTGCCACCAACAAATGGCTGA
AATTGCTGTAAATGCTGTCCTGATGGTAGCAGATATGGAACGAAGAGATGTTGACTTTGAGCTAATCAAAGTAGAAGGCA
AAGTAGGAGGAAGACTTGAAAATACTCAGCTCATTAAGGGAGTAATTGTGGATAAGGATTTTAGTCATCCACAAATGCCT
AAAGAAGTGAAAAATGCTAGGATTGAAGTTCTTACTTGTCCATTTGATCCACCTAAACCAAAAACTAAACATAAGCTTGA
TGTTACTTCTGTAGAAGATTACAGAGCCCTACAGAAATATGAAAGGGAGAAGTTTGAAGAGATGATTGAACAAATTAAAC
TCACTGGTGCAAACCTAGCTATTTGCCAGTGGGGCTTTGATGATGAAGCAAATCAATTACTCCTTCAGAATAAGTTATCT
GCTGTCCGTTGGGTAGGGGGACCGGAAATTGAACTGATTGCCATTGCAACGGGAAGGCGCATTGTTCCACGGTTCTCTGA
ACTTACATCTGAGAAACTTGGTTTTGTTGGTCTTGTGAAAGAGATTTCTTTTGGCACAACAAAAGACAAAATGCTCGTTA
TAGAGAAATGTCGGAACTCCAGGGCTGTGACCATATTCATTAGAGGAGGAAATAAAATGATCATTGAAGAAGCAAAACGA
TCTCTTCATGATGCTCTTTGTGTGATCAGAAACCTAGTTTGTGATAATCGTGTGGTATATGGAGGTGGTGCAGCTGAAAT
ATCTTGTGCTTTGGCAGCTAGTGAAGAAGTTGATAAGTGTCCTTCTTTGGAGCAATATACTATGAGAGCTTTTGCAGATT
CATTAGAGGTCATTCCCATGGCCCTTTCTGAAAATAGTGGTATGAATCCCATCCAAACTATGACTGATGTACGGGCCAGA
CAAGTGAAAGAAATGAATCCTGCCCGTGGCATTGACTGTTTGCATAAGGGTACAAATGATATGAGACAACAACATGTGAT
AGAAACTTTGGCAAAAAGCAACAGATTTCTCTTGCAACACAAATGGTCAAGATGATTCTGAAGATTGATGATATTCGCAA
ACCAGGAGAATCTGAAGAA

Alignment

ORF - retro_mdom_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSMGTLAFDEYGRPFLIIKDQERKSRLMGLEALKSHIMAAKAVSNTMRTSLGPNGLDKMMVDKDGDVTV
          MSSMGTL.FDEYGRPFLIIKDQERKS.LMGLEALKSHIMAAKAVSNTMRTSLGPNGLDKMMVDKDGDVTV
Retrocopy MSSMGTLEFDEYGRPFLIIKDQERKSHLMGLEALKSHIMAAKAVSNTMRTSLGPNGLDKMMVDKDGDVTV

Parental  TNDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQA
          TNDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQA
Retrocopy TNDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQA

Parental  ARIAIEHLDKISESFPVDVGNTEPLIQTAKTTLGSKVVNSCHQQMAEIAVNAVLTVADMERRDVDFELIK
          ARIAIEHLDKISESFPVDVGNTEPLIQTAKTTLGSKVVNSCHQQMAEIAVNAVL.VADMERRDVDFELIK
Retrocopy ARIAIEHLDKISESFPVDVGNTEPLIQTAKTTLGSKVVNSCHQQMAEIAVNAVLMVADMERRDVDFELIK

Parental  VEGKVGGRLEDTQLIKGVIVDKDFSHPQMPKEVKNARIAILTCPFEPPKPKTKHKLDVTSVEDYRALQKY
          VEGKVGGRLE.TQLIKGVIVDKDFSHPQMPKEVKNARI..LTCPF.PPKPKTKHKLDVTSVEDYRALQKY
Retrocopy VEGKVGGRLENTQLIKGVIVDKDFSHPQMPKEVKNARIEVLTCPFDPPKPKTKHKLDVTSVEDYRALQKY

Parental  EKEKFEEMIEQIKLTGANLAICQWGFDDEANHLLLQNKLPAVRWVGGPEIELIAIATGGRIVPRFSELTS
          E.EKFEEMIEQIKLTGANLAICQWGFDDEAN.LLLQNKL.AVRWVGGPEIELIAIATG.RIVPRFSELTS
Retrocopy EREKFEEMIEQIKLTGANLAICQWGFDDEANQLLLQNKLSAVRWVGGPEIELIAIATGRRIVPRFSELTS

Parental  EKLGFAGLVKEISFGTTKDKMLVIEKCRNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLVRDNRVVY
          EKLGF.GLVKEISFGTTKDKMLVIEKCRNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLV.DNRVVY
Retrocopy EKLGFVGLVKEISFGTTKDKMLVIEKCRNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLVCDNRVVY

Parental  GGGAAEISCALAVSEEADKCPSLEQYAMRAFADALEVIPMALSENSGMNPIQTMTDVRARQVKEMNPALG
          GGGAAEISCALA.SEE.DKCPSLEQY.MRAFAD.LEVIPMALSENSGMNPIQTMTDVRARQVKEMNPA.G
Retrocopy GGGAAEISCALAASEEVDKCPSLEQYTMRAFADSLEVIPMALSENSGMNPIQTMTDVRARQVKEMNPARG

Parental  IDCLHKGTNDMRQQHVIETLI-GKKQQISLATQMVRMILKIDDIRKPGESEE
          IDCLHKGTNDMRQQHVIETL...K.Q.ISLATQMV.MILKIDDIRKPGESEE
Retrocopy IDCLHKGTNDMRQQHVIETLA<KKQQ-ISLATQMVKMILKIDDIRKPGESEE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_861 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_861 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017889	1 retrocopy	retro_btau_1432,
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516,
Homo sapiens	ENSG00000150753	2 retrocopies	retro_hsap_1219, retro_hsap_3230,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197,
Myotis lucifugus	ENSMLUG00000007977	1 retrocopy	retro_mluc_1735,
Macaca mulatta	ENSMMUG00000020112	2 retrocopies	retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861 ,
Pongo abelii	ENSPPYG00000015342	2 retrocopies	retro_pabe_1012, retro_pabe_2678,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,