RetrogeneDB ID: retro_chof_366

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_100478:1898..3737(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSCHOG00000001608
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_chof_366
ATGGCGGCCTCAGCGAAAAAGAAGAATAAGAAGGGGAAGACTATCTCCCTAACAGACTTCCTGGCCGATGATGGGGGGAC
TGGTGGAGGAAGCACCTATGTTCCCAAGCCAGTCAGCTGGGCTGATGAAACAGATGATCTGGAAGGAGATGTTTCAACCA
CTTGGCACAGTAACGATGATGATGTGTATAGAGCACCTCCCAATTTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTG
CTCGGGAACCCAACATCGACCGGAGCCATCTTCCCCAATCACCACCCTACACTGCTTTTCTAGGGAACCTGCCCTATGAT
GTGACTGAAGATTCCATTAAGGAATTCTTCAGAGGATTGAATATCAGTGCAGTGTGTTTACCACGTGAACCCAGCAATCC
AGAGAGGCTGAAAGGTTTTGGTTATGCTGAGTTTGAGGACCTGGATTCCCTGTTCAGTGCCCTGAGCCTCAATGAAGAGT
CTCTAGGTAACAGGAGAATTCAAGTGGATGTTGCTGATCAAGCATAGGATAAAGACAGGGATGATCGTTCTTTTGGCAGA
GATAGAAATCGGGATTCTGACAAAACAGATACAGATTGGAGGGCCCGTCCTGCCACAGACAGCTTTGATGACTACCCACC
TAGAAGAGGTGATGATAGCTTTGGAGACAACTATCGTGATCGTTATGATTCAGACCGGTATCGTGATGGCTATCGTGACA
GTTATCGTGACGGCCCAAGCCGGGATATGGATCGATATGGAGGCCGGGATCGCTATGATGACCGAGGCAGCAGAGACTAT
GATAGAGGCTATGACTCCAGGATAGGCAGTGGCAGAAGAGCAATTGGTAGTGGGTACCCAGGGGTGATGACTACAGAGGA
GGCGGGGACCGCTATGAAGGCCGCTACGACAGCCGGGATGATGGGTCACGGAGCTCTAGAGATGATTACTCTCGAGATGA
TTATAGGCATGATGACAGAGGTCCCCCCCAAAGACCCAAACTGAATCTAAAGCCTCAGAGTACTCCTAAGGAAGATGATT
CCTCTGTTAGGACTTCCCAGCCAGTTGAGCAGCTTCCATCTTTGGAGGAGCAAAGCCTGTGGACACGGCTGCTAGAGAAC
GGGAAGTGGAACAACGGCTACAGAAGGAACAAGAGAAATTGCAGCGTCAGCTGGATGAGCCAAAACTTCAACGACGGCCT
CGGGAAAGACACCCAAGTTGGCGAAGTGAAGAAACTCAGGAACGCAAATGGTCGAGGACAGGAAGTGAGTCATCACAGAC
TGGGACCTCCGCCACATATGGCAGAAGTAAGTCAGATCAGGATTCACGAAGGAGAGGTGAGAAGTCTCTGGAAAATGAAA
CCCTCAGTAAGGAAGAAGACTGTCACTCTCCAACTTCCAAGCCTCCCAAATCTGACCAGCCTCTAAAGGTAATGCCAGCC
CCTCCACCAAAGAATGCTTGGGTGAAGCGAAGTTCTAATCCTCCTGCTCGATCTCAGAGCTCAGGAACAGAGTAGCAATC
TCCTACAAGTGGTGGAAAAATAGCTTCAGTTCAACCATCTGAGGAAGGACCAGCAAGAAAAGATGAAAACAAAGTAGATG
GGGTGAGTGTCCCAAAAGGCCAAAGTGGGAACTCTGTCCGTGGTCCAGGAGATGGAGGGAGCAAAGACCACTGGAAGGAG
TCTGATAGGAAAGATGGCAAAAAGGATCAAGACTCTAGATCTGCACCTGAGCCAAAGAAAACTGAAGAAAATCCAGCCTC
TAAGTTCAGTTCTGCAAGCAAGTATGCTGCTCTCTCAGTTGATGGTGAAGATGAAAACGAGGGGGAAGATTACACCGAA

Alignment

ORF - retro_chof_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAXXKKKNKKGKTISLTDFLAEDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAP-PI-
          MAA..KKKNKKGKTISLTDFLA.DGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAP.PI.
Retrocopy MAASAKKKNKKGKTISLTDFLADDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAP>PI>

Parental  DRSILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEDSIKEFFRGLNISAVRLPREPSNPERLKG
          DRSILPTAPRAAREPNIDRS.LP.SPPYTAFLGNLPYDVTEDSIKEFFRGLNISAV.LPREPSNPERLKG
Retrocopy DRSILPTAPRAAREPNIDRSHLPQSPPYTAFLGNLPYDVTEDSIKEFFRGLNISAVCLPREPSNPERLKG

Parental  FGYAEFEDLDSLFSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSF
          FGYAEFEDLDSLFSALSLNEESLGNRRI.VDVADQA.DKDRDDRSFGRDRNRDSDKTDTDWRARPATDSF
Retrocopy FGYAEFEDLDSLFSALSLNEESLGNRRIQVDVADQA*DKDRDDRSFGRDRNRDSDKTDTDWRARPATDSF

Parental  DDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGR
          DDYPPRRGDDSFGD.YRDRYDSDR............P.RDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGR
Retrocopy DDYPPRRGDDSFGDNYRDRYDSDRXXXXXXXXXXXXPSRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGR

Parental  RAFGSGY-RRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDS
          RA.GSGY..R.DDYRGGGDRYE.RYD.RDD.S............R.DDRGPPQRPKLNLKP.STPKEDDS
Retrocopy RAIGSGY<PRGDDYRGGGDRYEGRYDSRDDGSRXXXXXXXXXXXRHDDRGPPQRPKLNLKPQSTPKEDDS

Parental  SASTSQ-SSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERE
          S..TSQ..S.AASIFGGAKPVDTAAREREVE.RLQKEQEKLQRQLDEPKL.RRPRERHPSWRSEETQER.
Retrocopy SVRTSQ<AS*AASIFGGAKPVDTAAREREVEQRLQKEQEKLQRQLDEPKLQRRPRERHPSWRSEETQERK

Parental  RSRTGSESSQTGTSATSGRNARRRES----EKSLENETLSKEEDCHSPTSKPPKSDQPLKVMPAPPPKEN
          .SRTGSESSQTGTSAT.GR......S....EKSLENETLSKEEDCHSPTSKPPKSDQPLKVMPAPPPK.N
Retrocopy WSRTGSESSQTGTSATYGRSKSDQDSRRRGEKSLENETLSKEEDCHSPTSKPPKSDQPLKVMPAPPPK-N

Parental  AWVKRSSNPPARSQSSETEQQSPTSSGGKVASVQPSEEGPARKDENKVDGVSVPKGQSGNSVRGPGDGGS
          AWVKRSSNPPARSQSS.TE.QSPT.SGGK.ASVQPSEEGPARKDENKVDGVSVPKGQSGNSVRGPGDGGS
Retrocopy AWVKRSSNPPARSQSSGTE*QSPT-SGGKIASVQPSEEGPARKDENKVDGVSVPKGQSGNSVRGPGDGGS

Parental  KDHWKESDRKDGKKDQDSRSAPEPKKTEENPASKFSSASKYAALSVDGEDENEGEDYTE
          KDHWKESDRKDGKKDQDSRSAPEPKKTEENPASKFSSASKYAALSVDGEDENEGEDYTE
Retrocopy KDHWKESDRKDGKKDQDSRSAPEPKKTEENPASKFSSASKYAALSVDGEDENEGEDYTE

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_366 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366 ,
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,