RetrogeneDB ID: retro_chof_2000

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44900:10463..11608(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSCHOG00000007401
• Aliases: None
• Description: heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]

Sequence

>retro_chof_2000
ATAGGGCCAAAGAGAAGAACAGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACTGTTGG
AAAATCAATTGACTTGAAGGATAAATATAAAAATATTGGTGCTAAACTTGTTCAGGATGTTGCCAATAACACAAACGAAG
AGGCTGGGGATGGTACCACCACTGCTACTGTACTGGCACACTCTATTGCCAAGGAAGGGTTTGATAAGGTTAGCAAAGGT
GCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTAATTGCTGAACTTAAGAAACAGTCAAAACC
TGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTATAATTTCTTCAAACAGAGATAAAGAAATTGGCAATATCATATCTG
ATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGATGGAAAAACATTGAATGATGAATTAGAAATTATT
GAAGGCATGAAGTTTAATCTGGGTGATATTTCTCCATATTTTATTAATACATCAAAAGATCAGAAATGTGAATTCCAGGA
TGCCTATGTTCTGTTGAGTGAAAAGAAAATTTCTAGTGTCCAATGCATTGTACCTGCTCTTGAAATTGCCAATGCTCACC
GTAAGCCCTTGGTGATAATTGCCAAAGATGTTGACAGAGAAGCTCTAAGCACACTTGTTTTGAATAGGCTGAAAGTTGGT
CTTCAGGTTGTAGCAGTCAAAGCTCCAGGTTTTGGTGACAATAGAAAGAACCAGCTTAAAGATATGGCTATTGCTACTGG
TGGGGCAGTGTTTGGAGAAGAGGGGTTGACTCTAAACCTTGAAGATGTTCAGCCCCATGATTTGGGAAAAGTTGGAGAGG
TCATAGTGACCAAAGATGATGCCATGCTCCTGAAAGGAAAAGGTGACAAGACGCAAATTGAAAAACGTATTCAAGAATAA
TTGAGCAGTTAGATGTCACAACCAGTGAACACGAAAAGGAAAAACTAAATGAACATCTAGCAAAACTTTCAGATGGAGTA
GCTGTGCTGCAGGCTGGTGGAACAAGCGATGTGGAAGTGAATGAAAAGAAAGACAGAGTTACAGATGCACTCAATGCTAC
ATGAGCTGCTGTTGAAGAAGGCATT

Alignment

ORF - retro_chof_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.73 %
• Parental protein coverage: 73.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGPKGRTVIIEQSWGSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIA
          .GPK.RTVIIEQSWGSPKVTKDGVTV.KSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLA.SIA
Retrocopy IGPKRRTVIIEQSWGSPKVTKDGVTVGKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLAHSIA

Parental  KEGFEKISKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVG
          KEGF.K.SKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVA.IS.N.DKEIGNIISDAMKKVG
Retrocopy KEGFDKVSKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVAIISSNRDKEIGNIISDAMKKVG

Parental  RKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIA
          RKGVITVKDGKTLNDELEIIEGMKF..G.ISPYFINTSK.QKCEFQDAYVLLSEKKISSVQ.IVPALEIA
Retrocopy RKGVITVKDGKTLNDELEIIEGMKFNLGDISPYFINTSKDQKCEFQDAYVLLSEKKISSVQCIVPALEIA

Parental  NAHRKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNL
          NAHRKPLVIIA.DVD.EALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNL
Retrocopy NAHRKPLVIIAKDVDREALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNL

Parental  EDVQSHDLGKVGEVIVTKDDAMLLKGKGDKTQIEKRIQE-IIEQLDVTTSEYEKEKLNERLAKLSDGVAV
          EDVQ.HDLGKVGEVIVTKDDAMLLKGKGDKTQIEKRIQE.IIEQLDVTTSE.EKEKLNE.LAKLSDGVAV
Retrocopy EDVQPHDLGKVGEVIVTKDDAMLLKGKGDKTQIEKRIQE<IIEQLDVTTSEHEKEKLNEHLAKLSDGVAV

Parental  LKVGGTSDVEVNEKKDRVTDALNATRAA-EEGI
          L..GGTSDVEVNEKKDRVTDALNAT.AA.EEGI
Retrocopy LQAGGTSDVEVNEKKDRVTDALNAT*AAVEEGI

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_2000 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 17 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni	ENSCHOG00000007401	5 retrocopies	retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000 , retro_chof_2397,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pteropus vampyrus	ENSPVAG00000008306	1 retrocopy	retro_pvam_250,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus	ENSSTOG00000028470	1 retrocopy	retro_itri_224,
Tarsius syrichta	ENSTSYG00000000513	6 retrocopies	retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,