RetrogeneDB ID: retro_chof_1912

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42096:1663..2353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSCHOG00000010861
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_chof_1912
ATGGTGGAATCCATGAAGAAAGTAGCAGGGATGGATGTGGAGTTGACAGTTGAAGAAAGAAACCTACTATCTGTTGCATA
TAAAAATGTGATTGGAGCCAGAAGAGCCTCCTGGAGAATAATTAGCAGCATTGAACAGAAAGAAGAAAACAAGGGAGGAG
AAGACAAACTAAAAATGATTCGGGAATATTGGCAAATGGTTGAGACTGAACTAAAGTTAATCTGTTGTGACATTCTGGAT
GTACTGGACAAACATCTGATTCCAGCAGCTAACACTGGCGAGTCCAAGATTTTCTATTATAAAATGAAAGGAGATTACCA
CAGGTATCTGGCTGATTTGCCACAGGAATGACAGGAGAGCTGCAGAGACAGCCTAGTGCTTATAAGCTGCTAGTGATATT
GCATGACAGACTTTCCACCAACGCATCCCATTCGCTTAGGTCTTGCTCTCAATTCTTCTGTATTCTACTATGAAATTCTT
AATTCCCCTGACCGTGCCTGCAGGTCGGCAAAAGCAGCTTTTGATGATGCAGTTGCAGAACTGGATACCCTGAGTGAAGA
AAGCTATAAGGACTCTACACTTATCATGCAGTTGTTATGTGATAATCTGACACTATGGACTTCAGACATGCAGGGTGATG
GTGAAGAGCAGAATAAAGAAGCGCTGCAGGATGTGGAAGATGAAAATCAG

Alignment

ORF - retro_chof_1912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MVESMKKVAGMGV-LTVDERNLLSVAYKNVIGARRASWKIISSIEQKEENKGGEDELKMIWEYRQVVETE
          MVESMKKVAGM.V.LTV.ERNLLSVAYKNVIGARRASW.IISSIEQKEENKGGED.LKMI.EY.Q.VETE
Retrocopy MVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYWQMVETE

Parental  LKLICCDFLDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAE-FATG-NDRKEAAE-NSLV-AYK-AASD
          LKLICCD.LDVLDKHLIPAANTGESK.FYYKMKGDYHRYLA..FATG.NDR..AAE..SLV.AYK.AASD
Retrocopy LKLICCDILDVLDKHLIPAANTGESKIFYYKMKGDYHRYLAD<FATG<NDRR-AAE<DSLV<AYK<AASD

Parental  IA-MTEPPPTHPIRLGLALDFSVFYYEIPNSPDRACRLAKAAFDDAIAELGTLSEESYKDSALIMQLLRD
          IA.MT..PPTHPIRLGLAL..SVFYYEI.NSPDRACR.AKAAFDDA.AEL.TLSEESYKDS.LIMQLL.D
Retrocopy IA<MTDFPPTHPIRLGLALNSSVFYYEILNSPDRACRSAKAAFDDAVAELDTLSEESYKDSTLIMQLLCD

Parental  NLTLWTSDMQGDGEEQNKEALQDVEDENQ
          NLTLWTSDMQGDGEEQNKEALQDVEDENQ
Retrocopy NLTLWTSDMQGDGEEQNKEALQDVEDENQ

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_1912 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 22 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000002798	9 retrocopies	retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Choloepus hoffmanni	ENSCHOG00000004661	13 retrocopies	retro_chof_136, retro_chof_1427, retro_chof_1605, retro_chof_1835, retro_chof_2026, retro_chof_2115, retro_chof_2134, retro_chof_2233, retro_chof_429, retro_chof_481, retro_chof_489, retro_chof_527, retro_chof_863,
Choloepus hoffmanni	ENSCHOG00000005782	15 retrocopies	retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912 , retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Dasypus novemcinctus	ENSDNOG00000003808	2 retrocopies	retro_dnov_1452, retro_dnov_2602,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Macropus eugenii	ENSMEUG00000015460	12 retrocopies	retro_meug_1290, retro_meug_1396, retro_meug_1536, retro_meug_16, retro_meug_1926, retro_meug_196, retro_meug_2153, retro_meug_2163, retro_meug_835, retro_meug_9, retro_meug_982, retro_meug_986,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,